Starting phenix.real_space_refine on Wed Apr 10 13:13:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppv_17817/04_2024/8ppv_17817_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppv_17817/04_2024/8ppv_17817.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppv_17817/04_2024/8ppv_17817_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppv_17817/04_2024/8ppv_17817_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppv_17817/04_2024/8ppv_17817_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppv_17817/04_2024/8ppv_17817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppv_17817/04_2024/8ppv_17817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppv_17817/04_2024/8ppv_17817_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ppv_17817/04_2024/8ppv_17817_updated.pdb" } resolution = 3.02 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 36 5.49 5 Mg 3 5.21 5 S 80 5.16 5 C 12459 2.51 5 N 3278 2.21 5 O 3766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 178": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 301": "OD1" <-> "OD2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B ASP 328": "OD1" <-> "OD2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B GLU 491": "OE1" <-> "OE2" Residue "B GLU 560": "OE1" <-> "OE2" Residue "B GLU 698": "OE1" <-> "OE2" Residue "B TYR 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 812": "OD1" <-> "OD2" Residue "B GLU 959": "OE1" <-> "OE2" Residue "B ASP 960": "OD1" <-> "OD2" Residue "B PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1057": "OD1" <-> "OD2" Residue "B GLU 1191": "OE1" <-> "OE2" Residue "B ASP 1207": "OD1" <-> "OD2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "D PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D ASP 153": "OD1" <-> "OD2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E ASP 42": "OD1" <-> "OD2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E GLU 182": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19625 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3565 Classifications: {'peptide': 447} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 415} Chain: "B" Number of atoms: 9501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 9501 Classifications: {'peptide': 1188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 65, 'TRANS': 1121} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1939 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 7, 'TRANS': 238} Chain: "D" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1939 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 7, 'TRANS': 238} Chain: "E" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1939 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 7, 'TRANS': 238} Chain: "P" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 388 Unusual residues: {' GS': 1, 'C7R': 1} Classifications: {'DNA': 17, 'undetermined': 2} Link IDs: {'rna3p': 15, None: 3} Not linked: pdbres=" DT P 16 " pdbres=" GS P 17 " Not linked: pdbres=" GS P 17 " pdbres="C7R P 18 " Not linked: pdbres="C7R P 18 " pdbres="PST P 19 " Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 15 Chain: "T" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 348 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8976 SG CYS B 706 99.299 108.701 88.783 1.00 60.60 S ATOM 8998 SG CYS B 709 98.993 109.795 92.373 1.00 76.84 S ATOM 9063 SG CYS B 718 95.887 109.219 90.378 1.00 63.16 S ATOM 9084 SG CYS B 721 98.071 112.226 89.529 1.00 68.12 S ATOM 9167 SG CYS B 731 104.284 84.855 89.714 1.00 77.87 S ATOM 9191 SG CYS B 734 105.794 86.012 92.956 1.00 79.37 S ATOM 9319 SG CYS B 750 107.712 86.393 89.696 1.00 73.69 S ATOM 9341 SG CYS B 753 107.390 82.977 91.184 1.00 91.05 S ATOM 12332 SG CYS B1123 69.701 72.187 96.431 1.00 82.05 S ATOM 12460 SG CYS B1139 70.975 69.261 98.030 1.00 88.47 S ATOM 12480 SG CYS B1142 71.334 73.421 99.098 1.00 92.24 S Time building chain proxies: 10.57, per 1000 atoms: 0.54 Number of scatterers: 19625 At special positions: 0 Unit cell: (120.4, 144.48, 147.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 80 16.00 P 36 15.00 Mg 3 11.99 O 3766 8.00 N 3278 7.00 C 12459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 619 " distance=2.85 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.02 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 718 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 709 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 706 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 721 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 750 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 734 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 731 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 753 " pdb=" ZN B1303 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1142 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1123 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1139 " Number of angles added : 12 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4428 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 73 helices and 24 sheets defined 29.8% alpha, 19.8% beta 10 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 8.80 Creating SS restraints... Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 220 through 245 removed outlier: 3.715A pdb=" N ILE A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.972A pdb=" N LYS A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 387 through 393 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 424 through 437 removed outlier: 4.643A pdb=" N ASN A 437 " --> pdb=" O ASN A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 472 No H-bonds generated for 'chain 'A' and resid 469 through 472' Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.726A pdb=" N GLU A 502 " --> pdb=" O ARG A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 526 Proline residue: A 516 - end of helix Proline residue: A 519 - end of helix Processing helix chain 'A' and resid 585 through 589 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'B' and resid 6 through 31 removed outlier: 3.851A pdb=" N ILE B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 95 through 110 Processing helix chain 'B' and resid 117 through 120 No H-bonds generated for 'chain 'B' and resid 117 through 120' Processing helix chain 'B' and resid 145 through 149 removed outlier: 3.518A pdb=" N SER B 149 " --> pdb=" O PRO B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 168 Processing helix chain 'B' and resid 178 through 194 Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 243 through 250 removed outlier: 3.815A pdb=" N VAL B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 273 through 282 Processing helix chain 'B' and resid 312 through 323 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 369 through 375 Processing helix chain 'B' and resid 420 through 425 Processing helix chain 'B' and resid 443 through 449 Processing helix chain 'B' and resid 460 through 475 removed outlier: 3.971A pdb=" N LEU B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 497 Processing helix chain 'B' and resid 501 through 509 Processing helix chain 'B' and resid 518 through 527 Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 545 through 558 Processing helix chain 'B' and resid 579 through 591 removed outlier: 6.226A pdb=" N ASP B 584 " --> pdb=" O GLU B 580 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER B 585 " --> pdb=" O LYS B 581 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LYS B 586 " --> pdb=" O LEU B 582 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ARG B 587 " --> pdb=" O GLY B 583 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 589 " --> pdb=" O SER B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 614 removed outlier: 4.055A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 612 " --> pdb=" O PRO B 608 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU B 613 " --> pdb=" O TRP B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 639 Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 740 through 745 removed outlier: 3.668A pdb=" N GLY B 745 " --> pdb=" O SER B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 778 Processing helix chain 'B' and resid 802 through 811 Processing helix chain 'B' and resid 842 through 848 Processing helix chain 'B' and resid 877 through 896 removed outlier: 3.723A pdb=" N LYS B 885 " --> pdb=" O ARG B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 911 No H-bonds generated for 'chain 'B' and resid 909 through 911' Processing helix chain 'B' and resid 945 through 951 removed outlier: 3.696A pdb=" N LYS B 951 " --> pdb=" O PHE B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 971 Processing helix chain 'B' and resid 997 through 999 No H-bonds generated for 'chain 'B' and resid 997 through 999' Processing helix chain 'B' and resid 1004 through 1006 No H-bonds generated for 'chain 'B' and resid 1004 through 1006' Processing helix chain 'B' and resid 1015 through 1023 removed outlier: 3.890A pdb=" N TYR B1022 " --> pdb=" O TYR B1018 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU B1023 " --> pdb=" O GLU B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1030 Processing helix chain 'B' and resid 1037 through 1040 Processing helix chain 'B' and resid 1067 through 1070 Processing helix chain 'B' and resid 1074 through 1087 Processing helix chain 'B' and resid 1093 through 1118 removed outlier: 6.847A pdb=" N GLU B1098 " --> pdb=" O HIS B1094 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS B1104 " --> pdb=" O ILE B1100 " (cutoff:3.500A) Proline residue: B1107 - end of helix removed outlier: 4.143A pdb=" N THR B1117 " --> pdb=" O LEU B1113 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG B1118 " --> pdb=" O ARG B1114 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1155 No H-bonds generated for 'chain 'B' and resid 1152 through 1155' Processing helix chain 'B' and resid 1159 through 1168 Processing helix chain 'B' and resid 1173 through 1189 removed outlier: 3.552A pdb=" N ARG B1184 " --> pdb=" O CYS B1180 " (cutoff:3.500A) Processing helix chain 'B' and resid 1209 through 1215 Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 73 through 81 Processing helix chain 'C' and resid 138 through 151 removed outlier: 3.825A pdb=" N LEU C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 73 through 82 removed outlier: 3.979A pdb=" N ARG D 82 " --> pdb=" O LYS D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 202 through 208 Processing helix chain 'E' and resid 10 through 22 Processing helix chain 'E' and resid 73 through 82 removed outlier: 3.843A pdb=" N ARG E 82 " --> pdb=" O LYS E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 151 removed outlier: 4.204A pdb=" N LEU E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 208 Processing sheet with id= A, first strand: chain 'A' and resid 316 through 321 removed outlier: 6.743A pdb=" N GLU A 286 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS A 276 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE A 284 " --> pdb=" O LYS A 276 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU A 278 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLY A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N PHE A 329 " --> pdb=" O PHE A 297 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N ALA A 331 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LYS A 320 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE A 334 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA A 318 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 477 through 479 removed outlier: 6.219A pdb=" N MET A 444 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N TYR A 354 " --> pdb=" O LYS A 397 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU A 399 " --> pdb=" O TYR A 354 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 356 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE A 401 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 358 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 599 " --> pdb=" O LEU A 613 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASP A 603 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL A 609 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 565 through 569 removed outlier: 3.570A pdb=" N VAL A 485 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG A 487 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VAL A 199 " --> pdb=" O ARG A 487 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 42 through 44 removed outlier: 3.565A pdb=" N LEU B 920 " --> pdb=" O ALA B 961 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 217 through 219 removed outlier: 3.510A pdb=" N ASN B 124 " --> pdb=" O TYR B 142 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 350 through 354 removed outlier: 7.029A pdb=" N GLY B 437 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ARG B 353 " --> pdb=" O GLY B 437 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ALA B 439 " --> pdb=" O ARG B 353 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 365 through 367 Processing sheet with id= H, first strand: chain 'B' and resid 385 through 387 Processing sheet with id= I, first strand: chain 'B' and resid 414 through 417 removed outlier: 6.821A pdb=" N LYS B 408 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ILE B 433 " --> pdb=" O LYS B 408 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 596 through 599 removed outlier: 6.402A pdb=" N GLU B 562 " --> pdb=" O LYS B 573 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE B 575 " --> pdb=" O GLU B 560 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLU B 560 " --> pdb=" O ILE B 575 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 697 through 701 removed outlier: 3.564A pdb=" N ILE B 701 " --> pdb=" O ALA B 761 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 832 through 834 Processing sheet with id= M, first strand: chain 'B' and resid 872 through 875 removed outlier: 6.130A pdb=" N ARG B 931 " --> pdb=" O ILE B 873 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU B 875 " --> pdb=" O ARG B 931 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE B 933 " --> pdb=" O LEU B 875 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 3 through 8 removed outlier: 3.689A pdb=" N PHE C 3 " --> pdb=" O LYS C 93 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS C 93 " --> pdb=" O PHE C 3 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR C 88 " --> pdb=" O GLN C 104 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 26 through 31 removed outlier: 4.470A pdb=" N ALA C 27 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL C 71 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 35 through 41 removed outlier: 3.706A pdb=" N ARG C 238 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR C 231 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C 221 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP C 188 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 195 through 200 removed outlier: 6.179A pdb=" N SER C 154 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLU C 169 " --> pdb=" O SER C 154 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 60 through 62 removed outlier: 3.609A pdb=" N LYS D 60 " --> pdb=" O VAL D 6 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 26 through 31 removed outlier: 4.256A pdb=" N ALA D 27 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL D 71 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 35 through 41 removed outlier: 4.923A pdb=" N TYR D 232 " --> pdb=" O GLU D 216 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLU D 216 " --> pdb=" O TYR D 232 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL D 135 " --> pdb=" O ASP D 188 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP D 188 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU D 137 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU D 186 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 195 through 200 removed outlier: 3.803A pdb=" N THR D 195 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA D 159 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N SER D 154 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU D 169 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 60 through 63 removed outlier: 3.913A pdb=" N LYS E 60 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE E 3 " --> pdb=" O LYS E 93 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 67 through 72 removed outlier: 3.658A pdb=" N VAL E 71 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA E 27 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLU E 26 " --> pdb=" O MET E 41 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N MET E 41 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA E 28 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG E 39 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET E 38 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN E 52 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR E 231 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA E 132 " --> pdb=" O PHE E 221 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP E 188 " --> pdb=" O VAL E 135 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 195 through 200 removed outlier: 3.735A pdb=" N THR E 195 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N SER E 154 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLU E 169 " --> pdb=" O SER E 154 " (cutoff:3.500A) 696 hydrogen bonds defined for protein. 1944 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 8.60 Time building geometry restraints manager: 8.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6272 1.34 - 1.46: 3356 1.46 - 1.58: 10241 1.58 - 1.70: 67 1.70 - 1.82: 132 Bond restraints: 20068 Sorted by residual: bond pdb=" P GS P 17 " pdb=" S2P GS P 17 " ideal model delta sigma weight residual 2.124 1.477 0.647 2.00e-02 2.50e+03 1.05e+03 bond pdb=" P C7R P 18 " pdb=" SP2 C7R P 18 " ideal model delta sigma weight residual 2.121 1.479 0.642 2.00e-02 2.50e+03 1.03e+03 bond pdb=" P PST P 19 " pdb=" SP PST P 19 " ideal model delta sigma weight residual 1.914 1.478 0.436 2.00e-02 2.50e+03 4.76e+02 bond pdb=" P PST P 20 " pdb=" SP PST P 20 " ideal model delta sigma weight residual 1.914 1.478 0.436 2.00e-02 2.50e+03 4.76e+02 bond pdb=" P PST P 21 " pdb=" SP PST P 21 " ideal model delta sigma weight residual 1.914 1.478 0.436 2.00e-02 2.50e+03 4.75e+02 ... (remaining 20063 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.57: 750 106.57 - 113.44: 10925 113.44 - 120.30: 7431 120.30 - 127.16: 7902 127.16 - 134.02: 240 Bond angle restraints: 27248 Sorted by residual: angle pdb=" C1' GS P 17 " pdb=" N9 GS P 17 " pdb=" C4 GS P 17 " ideal model delta sigma weight residual 108.33 127.21 -18.88 3.00e+00 1.11e-01 3.96e+01 angle pdb=" N ASP D 235 " pdb=" CA ASP D 235 " pdb=" CB ASP D 235 " ideal model delta sigma weight residual 114.17 110.09 4.08 1.14e+00 7.69e-01 1.28e+01 angle pdb=" OP1 PST P 19 " pdb=" P PST P 19 " pdb=" SP PST P 19 " ideal model delta sigma weight residual 109.47 120.21 -10.74 3.00e+00 1.11e-01 1.28e+01 angle pdb=" OP1 GS P 17 " pdb=" P GS P 17 " pdb=" S2P GS P 17 " ideal model delta sigma weight residual 109.47 119.83 -10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" OP1 PST P 21 " pdb=" P PST P 21 " pdb=" SP PST P 21 " ideal model delta sigma weight residual 109.47 119.69 -10.22 3.00e+00 1.11e-01 1.16e+01 ... (remaining 27243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.19: 11546 34.19 - 68.37: 587 68.37 - 102.56: 37 102.56 - 136.75: 0 136.75 - 170.93: 1 Dihedral angle restraints: 12171 sinusoidal: 5291 harmonic: 6880 Sorted by residual: dihedral pdb=" CA GLU B1093 " pdb=" C GLU B1093 " pdb=" N HIS B1094 " pdb=" CA HIS B1094 " ideal model delta harmonic sigma weight residual -180.00 -152.94 -27.06 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA LYS B 980 " pdb=" C LYS B 980 " pdb=" N ARG B 981 " pdb=" CA ARG B 981 " ideal model delta harmonic sigma weight residual 180.00 154.24 25.76 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA LYS B 668 " pdb=" C LYS B 668 " pdb=" N PRO B 669 " pdb=" CA PRO B 669 " ideal model delta harmonic sigma weight residual 180.00 154.31 25.69 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 12168 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2642 0.061 - 0.122: 362 0.122 - 0.184: 41 0.184 - 0.245: 0 0.245 - 0.306: 5 Chirality restraints: 3050 Sorted by residual: chirality pdb=" C3' PST P 20 " pdb=" C4' PST P 20 " pdb=" O3' PST P 20 " pdb=" C2' PST P 20 " both_signs ideal model delta sigma weight residual False -2.35 -2.66 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C3' PST P 19 " pdb=" C4' PST P 19 " pdb=" O3' PST P 19 " pdb=" C2' PST P 19 " both_signs ideal model delta sigma weight residual False -2.35 -2.64 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C3' PST P 21 " pdb=" C4' PST P 21 " pdb=" O3' PST P 21 " pdb=" C2' PST P 21 " both_signs ideal model delta sigma weight residual False -2.35 -2.64 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 3047 not shown) Planarity restraints: 3387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 235 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C ASP D 235 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP D 235 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU D 236 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 518 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 519 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 519 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 519 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 53 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO E 54 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 54 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 54 " 0.024 5.00e-02 4.00e+02 ... (remaining 3384 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 35 2.39 - 3.02: 10901 3.02 - 3.65: 26792 3.65 - 4.27: 41302 4.27 - 4.90: 73297 Nonbonded interactions: 152327 Sorted by model distance: nonbonded pdb=" OD1 ASN A 450 " pdb="MG MG A 702 " model vdw 1.764 2.170 nonbonded pdb=" OD1 ASP A 360 " pdb="MG MG A 701 " model vdw 1.870 2.170 nonbonded pdb=" OD2 ASP A 404 " pdb="MG MG A 702 " model vdw 1.937 2.170 nonbonded pdb=" O ASP D 235 " pdb=" OD1 ASP D 235 " model vdw 2.135 3.040 nonbonded pdb=" N GLU E 26 " pdb=" OE1 GLU E 26 " model vdw 2.168 2.520 ... (remaining 152322 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 5.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.480 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 62.660 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 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 : 0.012 0.647 20068 Z= 0.810 Angle : 0.631 18.881 27248 Z= 0.317 Chirality : 0.045 0.306 3050 Planarity : 0.004 0.045 3387 Dihedral : 18.322 170.933 7740 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.00 % Rotamer: Outliers : 0.15 % Allowed : 21.33 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: -0.08 (0.18), residues: 2361 helix: 1.19 (0.20), residues: 713 sheet: 0.19 (0.23), residues: 540 loop : -0.98 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.005 0.001 HIS B 944 PHE 0.016 0.001 PHE B 467 TYR 0.012 0.001 TYR A 428 ARG 0.008 0.000 ARG E 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 200 time to evaluate : 2.209 Fit side-chains REVERT: C 84 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.6844 (ttpt) REVERT: E 174 GLU cc_start: 0.7632 (tt0) cc_final: 0.7398 (pt0) outliers start: 3 outliers final: 1 residues processed: 202 average time/residue: 0.3868 time to fit residues: 114.4414 Evaluate side-chains 192 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain C residue 84 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 95 optimal weight: 0.3980 chunk 184 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 112 optimal weight: 0.0980 chunk 137 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20068 Z= 0.249 Angle : 0.564 7.447 27248 Z= 0.295 Chirality : 0.046 0.173 3050 Planarity : 0.004 0.053 3387 Dihedral : 12.641 176.998 2937 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 1.75 % Allowed : 20.41 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: 0.07 (0.17), residues: 2361 helix: 1.18 (0.20), residues: 708 sheet: 0.54 (0.23), residues: 531 loop : -0.93 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.004 0.001 HIS B 533 PHE 0.013 0.001 PHE B 467 TYR 0.015 0.001 TYR B1047 ARG 0.003 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 209 time to evaluate : 2.344 Fit side-chains REVERT: B 491 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: B 824 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8573 (m-30) REVERT: C 238 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7608 (ttp-110) REVERT: D 41 MET cc_start: 0.8251 (mmm) cc_final: 0.7741 (mmm) REVERT: D 196 LYS cc_start: 0.7365 (ptpp) cc_final: 0.7132 (ptmt) REVERT: E 174 GLU cc_start: 0.7709 (tt0) cc_final: 0.7505 (pt0) outliers start: 36 outliers final: 18 residues processed: 235 average time/residue: 0.3947 time to fit residues: 136.5560 Evaluate side-chains 213 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 192 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 824 ASP Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1104 HIS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1161 THR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 166 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 214 optimal weight: 8.9990 chunk 231 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 172 optimal weight: 0.0270 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 GLN D 15 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20068 Z= 0.307 Angle : 0.584 8.336 27248 Z= 0.302 Chirality : 0.046 0.254 3050 Planarity : 0.005 0.060 3387 Dihedral : 12.582 175.807 2931 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.53 % Favored : 95.43 % Rotamer: Outliers : 3.07 % Allowed : 20.26 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2361 helix: 0.95 (0.20), residues: 708 sheet: 0.54 (0.23), residues: 531 loop : -1.04 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.006 0.001 HIS B 944 PHE 0.017 0.002 PHE B 467 TYR 0.016 0.002 TYR B 558 ARG 0.003 0.000 ARG E 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 202 time to evaluate : 2.222 Fit side-chains revert: symmetry clash REVERT: B 211 MET cc_start: 0.4560 (mtm) cc_final: 0.3855 (ttt) REVERT: B 491 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: B 652 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8898 (mm) REVERT: B 824 ASP cc_start: 0.8898 (OUTLIER) cc_final: 0.8600 (m-30) REVERT: B 1086 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8517 (ttmt) REVERT: C 84 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.6938 (ttpt) REVERT: C 238 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7740 (ttp-110) REVERT: D 41 MET cc_start: 0.8135 (mmm) cc_final: 0.7608 (mmm) REVERT: E 174 GLU cc_start: 0.7662 (tt0) cc_final: 0.7461 (pt0) outliers start: 63 outliers final: 35 residues processed: 254 average time/residue: 0.3633 time to fit residues: 138.6005 Evaluate side-chains 237 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 196 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 824 ASP Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1104 HIS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1161 THR Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain E residue 239 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 111 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 102 optimal weight: 0.0470 chunk 144 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 228 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 204 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 HIS ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20068 Z= 0.157 Angle : 0.494 8.252 27248 Z= 0.260 Chirality : 0.043 0.172 3050 Planarity : 0.004 0.055 3387 Dihedral : 12.408 172.243 2931 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.30 % Favored : 96.65 % Rotamer: Outliers : 2.48 % Allowed : 21.63 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.17), residues: 2361 helix: 1.21 (0.20), residues: 709 sheet: 0.69 (0.22), residues: 526 loop : -0.95 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 132 HIS 0.002 0.001 HIS A 560 PHE 0.010 0.001 PHE B 443 TYR 0.013 0.001 TYR B 558 ARG 0.002 0.000 ARG E 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 214 time to evaluate : 2.179 Fit side-chains REVERT: B 491 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: B 656 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8716 (ttt) REVERT: B 1086 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8200 (ttmt) REVERT: B 1187 ASP cc_start: 0.7764 (t0) cc_final: 0.7521 (m-30) REVERT: C 84 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.6950 (ttpt) REVERT: C 238 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7738 (ttp-110) REVERT: D 41 MET cc_start: 0.7967 (mmm) cc_final: 0.7646 (mmm) REVERT: E 39 ARG cc_start: 0.8579 (ttm110) cc_final: 0.8157 (ttm170) REVERT: E 66 GLU cc_start: 0.6052 (pp20) cc_final: 0.5520 (mp0) outliers start: 51 outliers final: 30 residues processed: 256 average time/residue: 0.3749 time to fit residues: 143.1437 Evaluate side-chains 230 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 195 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 485 ASN Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain E residue 239 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 204 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 20068 Z= 0.418 Angle : 0.646 9.488 27248 Z= 0.330 Chirality : 0.048 0.200 3050 Planarity : 0.005 0.061 3387 Dihedral : 12.595 169.076 2931 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.83 % Favored : 95.13 % Rotamer: Outliers : 3.80 % Allowed : 21.87 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -0.27 (0.17), residues: 2361 helix: 0.76 (0.19), residues: 706 sheet: 0.56 (0.22), residues: 533 loop : -1.16 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 132 HIS 0.007 0.001 HIS B 944 PHE 0.021 0.002 PHE B 467 TYR 0.020 0.002 TYR B 558 ARG 0.004 0.000 ARG B 647 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 193 time to evaluate : 2.570 Fit side-chains REVERT: A 360 ASP cc_start: 0.9105 (OUTLIER) cc_final: 0.8487 (m-30) REVERT: B 184 MET cc_start: 0.4406 (mtm) cc_final: 0.3480 (tpt) REVERT: B 491 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: B 824 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8610 (m-30) REVERT: B 1094 HIS cc_start: 0.6757 (OUTLIER) cc_final: 0.5984 (t-90) REVERT: C 238 ARG cc_start: 0.8130 (ptp-170) cc_final: 0.7812 (ttp-110) REVERT: D 23 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8571 (mm) REVERT: E 66 GLU cc_start: 0.6115 (pp20) cc_final: 0.5190 (pt0) outliers start: 78 outliers final: 52 residues processed: 261 average time/residue: 0.3551 time to fit residues: 139.9689 Evaluate side-chains 243 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 186 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 485 ASN Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 824 ASP Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 992 THR Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1094 HIS Chi-restraints excluded: chain B residue 1104 HIS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1161 THR Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain E residue 239 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 133 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 228 optimal weight: 0.9990 chunk 189 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20068 Z= 0.179 Angle : 0.508 8.115 27248 Z= 0.266 Chirality : 0.043 0.170 3050 Planarity : 0.004 0.054 3387 Dihedral : 12.424 167.547 2931 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.92 % Allowed : 23.09 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: -0.07 (0.17), residues: 2361 helix: 1.01 (0.20), residues: 703 sheet: 0.57 (0.22), residues: 533 loop : -1.03 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 132 HIS 0.003 0.001 HIS B 944 PHE 0.011 0.001 PHE B 467 TYR 0.014 0.001 TYR B 558 ARG 0.002 0.000 ARG B1089 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 198 time to evaluate : 2.455 Fit side-chains REVERT: B 491 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: B 656 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8691 (ttt) REVERT: B 1187 ASP cc_start: 0.7758 (t0) cc_final: 0.7423 (m-30) REVERT: B 1208 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8633 (tp) REVERT: C 84 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.6927 (ttpt) REVERT: C 194 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7032 (mm-30) REVERT: C 238 ARG cc_start: 0.8078 (ptp-170) cc_final: 0.7768 (ttp-110) REVERT: D 23 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8439 (mm) REVERT: D 26 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: D 41 MET cc_start: 0.8023 (mmm) cc_final: 0.7660 (mmm) REVERT: E 39 ARG cc_start: 0.8540 (ttm110) cc_final: 0.8161 (ttm170) REVERT: E 66 GLU cc_start: 0.6071 (pp20) cc_final: 0.5182 (pt0) outliers start: 60 outliers final: 42 residues processed: 245 average time/residue: 0.3598 time to fit residues: 132.3605 Evaluate side-chains 242 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 193 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 485 ASN Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 967 ASP Chi-restraints excluded: chain B residue 992 THR Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1104 HIS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1208 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain E residue 239 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 192 optimal weight: 0.4980 chunk 127 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20068 Z= 0.197 Angle : 0.513 8.157 27248 Z= 0.268 Chirality : 0.044 0.172 3050 Planarity : 0.004 0.056 3387 Dihedral : 12.425 165.523 2931 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.31 % Allowed : 22.60 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: 0.00 (0.17), residues: 2361 helix: 1.08 (0.20), residues: 703 sheet: 0.64 (0.23), residues: 528 loop : -1.00 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 132 HIS 0.004 0.001 HIS B 944 PHE 0.014 0.001 PHE B 467 TYR 0.016 0.001 TYR B 558 ARG 0.002 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 199 time to evaluate : 2.416 Fit side-chains REVERT: A 360 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8326 (m-30) REVERT: B 491 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: B 656 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.8691 (ttt) REVERT: B 824 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8633 (m-30) REVERT: B 1187 ASP cc_start: 0.7791 (t0) cc_final: 0.7481 (m-30) REVERT: B 1208 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8647 (tp) REVERT: C 84 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.6923 (ttpt) REVERT: C 178 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8216 (tttt) REVERT: C 194 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7029 (mm-30) REVERT: C 238 ARG cc_start: 0.8074 (ptp-170) cc_final: 0.7766 (ttp-110) REVERT: D 23 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8472 (mm) REVERT: D 26 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: D 41 MET cc_start: 0.8003 (mmm) cc_final: 0.7651 (mmm) REVERT: E 66 GLU cc_start: 0.5923 (pp20) cc_final: 0.5106 (pt0) outliers start: 68 outliers final: 52 residues processed: 253 average time/residue: 0.3606 time to fit residues: 136.9766 Evaluate side-chains 253 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 192 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 485 ASN Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 824 ASP Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1104 HIS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1208 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain E residue 239 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20068 Z= 0.195 Angle : 0.514 8.282 27248 Z= 0.267 Chirality : 0.043 0.174 3050 Planarity : 0.004 0.057 3387 Dihedral : 12.427 163.694 2931 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.46 % Allowed : 22.45 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: 0.02 (0.17), residues: 2361 helix: 1.11 (0.20), residues: 705 sheet: 0.64 (0.22), residues: 530 loop : -1.00 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 132 HIS 0.004 0.001 HIS B 944 PHE 0.013 0.001 PHE B 467 TYR 0.016 0.001 TYR B 558 ARG 0.007 0.000 ARG B1132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 193 time to evaluate : 2.106 Fit side-chains REVERT: A 360 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8314 (m-30) REVERT: B 211 MET cc_start: 0.4005 (tpt) cc_final: 0.3570 (ptt) REVERT: B 491 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: B 656 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8694 (ttt) REVERT: B 824 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8638 (m-30) REVERT: B 1187 ASP cc_start: 0.7841 (t0) cc_final: 0.7519 (m-30) REVERT: B 1208 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8641 (tp) REVERT: C 84 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.6945 (ttpt) REVERT: C 165 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7766 (m) REVERT: C 194 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7061 (mm-30) REVERT: C 238 ARG cc_start: 0.8070 (ptp-170) cc_final: 0.7760 (ttp-110) REVERT: D 23 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8482 (mm) REVERT: D 26 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: D 41 MET cc_start: 0.7989 (mmm) cc_final: 0.7638 (mmm) REVERT: E 66 GLU cc_start: 0.5949 (pp20) cc_final: 0.5154 (pt0) outliers start: 71 outliers final: 54 residues processed: 251 average time/residue: 0.3558 time to fit residues: 134.0841 Evaluate side-chains 254 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 190 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 485 ASN Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 565 ASN Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 824 ASP Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1104 HIS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1208 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain E residue 239 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 0.0370 chunk 198 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 191 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 overall best weight: 1.8664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN D 15 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20068 Z= 0.316 Angle : 0.584 8.806 27248 Z= 0.300 Chirality : 0.046 0.180 3050 Planarity : 0.005 0.059 3387 Dihedral : 12.582 159.697 2931 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.51 % Allowed : 22.70 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: -0.18 (0.17), residues: 2361 helix: 0.93 (0.20), residues: 703 sheet: 0.54 (0.23), residues: 522 loop : -1.11 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 132 HIS 0.007 0.001 HIS B 944 PHE 0.019 0.002 PHE B 467 TYR 0.020 0.002 TYR B 558 ARG 0.005 0.000 ARG B1132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 194 time to evaluate : 2.278 Fit side-chains REVERT: A 360 ASP cc_start: 0.8993 (OUTLIER) cc_final: 0.8406 (m-30) REVERT: B 211 MET cc_start: 0.4769 (tpt) cc_final: 0.3799 (mtm) REVERT: B 491 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: B 656 MET cc_start: 0.9301 (OUTLIER) cc_final: 0.8849 (ttt) REVERT: B 824 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8570 (m-30) REVERT: B 1092 ASP cc_start: 0.7603 (t0) cc_final: 0.7387 (t0) REVERT: B 1208 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8703 (tp) REVERT: C 84 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.6872 (ttpt) REVERT: C 194 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7053 (mm-30) REVERT: C 238 ARG cc_start: 0.8092 (ptp-170) cc_final: 0.7781 (ttp-110) REVERT: D 23 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8556 (mm) REVERT: D 41 MET cc_start: 0.8104 (mmm) cc_final: 0.7701 (mmm) REVERT: E 66 GLU cc_start: 0.5995 (pp20) cc_final: 0.5205 (pt0) REVERT: E 227 MET cc_start: 0.8579 (ttp) cc_final: 0.8375 (ptm) outliers start: 72 outliers final: 54 residues processed: 257 average time/residue: 0.3524 time to fit residues: 136.8383 Evaluate side-chains 254 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 192 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 485 ASN Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 824 ASP Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1104 HIS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1208 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain E residue 239 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 0.0970 chunk 106 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 144 optimal weight: 0.0570 chunk 114 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 199 optimal weight: 3.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20068 Z= 0.175 Angle : 0.502 8.928 27248 Z= 0.262 Chirality : 0.043 0.173 3050 Planarity : 0.004 0.056 3387 Dihedral : 12.421 155.933 2931 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.02 % Allowed : 23.14 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % 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: 0.00 (0.17), residues: 2361 helix: 1.09 (0.20), residues: 705 sheet: 0.69 (0.23), residues: 510 loop : -1.02 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 132 HIS 0.003 0.001 HIS B 944 PHE 0.010 0.001 PHE B 443 TYR 0.015 0.001 TYR B 558 ARG 0.006 0.000 ARG B1132 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 202 time to evaluate : 2.574 Fit side-chains REVERT: B 211 MET cc_start: 0.4692 (tpt) cc_final: 0.3660 (mtm) REVERT: B 491 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: B 656 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8684 (ttt) REVERT: B 824 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8613 (m-30) REVERT: B 1208 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8644 (tp) REVERT: C 84 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.6882 (ttpt) REVERT: C 165 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7937 (p) REVERT: C 178 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8276 (tttt) REVERT: C 194 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7023 (mm-30) REVERT: C 238 ARG cc_start: 0.8061 (ptp-170) cc_final: 0.7754 (ttp-110) REVERT: D 23 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8482 (mm) REVERT: D 41 MET cc_start: 0.8012 (mmm) cc_final: 0.7657 (mmm) REVERT: E 66 GLU cc_start: 0.6052 (pp20) cc_final: 0.5260 (pt0) REVERT: E 227 MET cc_start: 0.8562 (ttp) cc_final: 0.8358 (ptm) outliers start: 62 outliers final: 50 residues processed: 252 average time/residue: 0.3569 time to fit residues: 135.4303 Evaluate side-chains 252 residues out of total 2054 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 194 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 485 ASN Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 664 GLU Chi-restraints excluded: chain B residue 730 VAL Chi-restraints excluded: chain B residue 753 CYS Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 824 ASP Chi-restraints excluded: chain B residue 841 SER Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1104 HIS Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1208 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain E residue 239 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 27 optimal weight: 0.0470 chunk 52 optimal weight: 0.7980 chunk 187 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 10 optimal weight: 0.0170 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.183221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.120037 restraints weight = 21700.702| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.19 r_work: 0.3206 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20068 Z= 0.153 Angle : 0.481 8.925 27248 Z= 0.251 Chirality : 0.043 0.173 3050 Planarity : 0.004 0.056 3387 Dihedral : 12.236 148.528 2931 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.58 % Allowed : 23.67 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.17), residues: 2361 helix: 1.27 (0.20), residues: 703 sheet: 0.73 (0.23), residues: 521 loop : -0.94 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 132 HIS 0.002 0.000 HIS B 944 PHE 0.011 0.001 PHE B 443 TYR 0.015 0.001 TYR B 558 ARG 0.006 0.000 ARG B1132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4520.57 seconds wall clock time: 83 minutes 5.37 seconds (4985.37 seconds total)