Starting phenix.real_space_refine on Wed Apr 10 15:49:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9f_36985/04_2024/8k9f_36985_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9f_36985/04_2024/8k9f_36985.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9f_36985/04_2024/8k9f_36985_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9f_36985/04_2024/8k9f_36985_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9f_36985/04_2024/8k9f_36985_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9f_36985/04_2024/8k9f_36985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9f_36985/04_2024/8k9f_36985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9f_36985/04_2024/8k9f_36985_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k9f_36985/04_2024/8k9f_36985_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 Fe 21 7.16 5 P 2 5.49 5 Mg 1 5.21 5 S 115 5.16 5 C 12962 2.51 5 N 3305 2.21 5 O 3500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 85": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B GLU 571": "OE1" <-> "OE2" Residue "B GLU 743": "OE1" <-> "OE2" Residue "B GLU 761": "OE1" <-> "OE2" Residue "B GLU 859": "OE1" <-> "OE2" Residue "B GLU 910": "OE1" <-> "OE2" Residue "B GLU 1022": "OE1" <-> "OE2" Residue "B GLU 1023": "OE1" <-> "OE2" Residue "B GLU 1025": "OE1" <-> "OE2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C GLU 337": "OE1" <-> "OE2" Residue "C PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 457": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 292": "OE1" <-> "OE2" Residue "F GLU 361": "OE1" <-> "OE2" Residue "F GLU 403": "OE1" <-> "OE2" Residue "G GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19906 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1763 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 13, 'TRANS': 204} Chain: "B" Number of atoms: 7350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 951, 7350 Classifications: {'peptide': 951} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 58, 'TRANS': 892} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 3655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3655 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 23, 'TRANS': 425} Chain: "D" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1350 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 15, 'TRANS': 159} Chain: "E" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1298 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 10, 'TRANS': 153} Chain: "F" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3128 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 20, 'TRANS': 376} Chain: "G" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 623 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 6, 'TRANS': 73} Chain: "I" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 305 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "A" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 215 Unusual residues: {'HEC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 32 Unusual residues: {' MG': 1, 'F3S': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'JLQ': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 99 Unusual residues: {'JL3': 1, 'JM9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7333 SG CYS B 797 44.501 87.882 66.555 1.00 36.72 S ATOM 8689 SG CYS B 972 47.397 88.353 69.815 1.00 21.24 S ATOM 8689 SG CYS B 972 47.397 88.353 69.815 1.00 21.24 S ATOM 7333 SG CYS B 797 44.501 87.882 66.555 1.00 36.72 S ATOM 7352 SG CYS B 800 48.418 85.757 65.059 1.00 10.80 S ATOM 7315 SG CYS B 794 45.507 82.829 69.293 1.00 20.73 S ATOM 8420 SG CYS B 934 58.611 89.152 63.063 1.00 20.48 S ATOM 7377 SG CYS B 804 55.595 86.553 60.458 1.00 4.73 S ATOM 8395 SG CYS B 931 58.474 83.540 63.167 1.00 0.00 S ATOM 7377 SG CYS B 804 55.595 86.553 60.458 1.00 4.73 S ATOM 8660 SG CYS B 968 54.561 86.783 65.194 1.00 27.57 S ATOM 8395 SG CYS B 931 58.474 83.540 63.167 1.00 0.00 S ATOM 8660 SG CYS B 968 54.561 86.783 65.194 1.00 27.57 S ATOM 7749 SG CYS B 850 61.378 77.497 63.606 1.00 0.00 S ATOM 7808 SG CYS B 858 64.708 73.411 61.503 1.00 30.00 S ATOM 7808 SG CYS B 858 64.708 73.411 61.503 1.00 30.00 S ATOM 8067 SG CYS B 892 59.968 72.656 61.256 1.00 14.29 S ATOM 7772 SG CYS B 853 62.306 73.027 66.302 1.00 1.90 S ATOM 7837 SG CYS B 862 69.470 73.617 53.738 1.00 6.21 S ATOM 8039 SG CYS B 888 64.556 73.311 53.774 1.00 14.82 S ATOM 7994 SG CYS B 882 66.463 76.955 50.207 1.00 30.00 S Time building chain proxies: 11.32, per 1000 atoms: 0.57 Number of scatterers: 19906 At special positions: 0 Unit cell: (130.2, 154.38, 104.16, 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) Fe 21 26.01 S 115 16.00 P 2 15.00 Mg 1 11.99 O 3500 8.00 N 3305 7.00 C 12962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.52 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B1104 " pdb="FE3 F3S B1104 " - pdb=" SG CYS B 888 " pdb="FE1 F3S B1104 " - pdb=" SG CYS B 862 " pdb="FE4 F3S B1104 " - pdb=" SG CYS B 882 " pdb=" SF4 B1101 " pdb="FE1 SF4 B1101 " - pdb=" SG CYS B 797 " pdb="FE2 SF4 B1101 " - pdb=" SG CYS B 972 " pdb="FE4 SF4 B1101 " - pdb=" SG CYS B 794 " pdb="FE3 SF4 B1101 " - pdb=" SG CYS B 800 " pdb=" SF4 B1102 " pdb="FE3 SF4 B1102 " - pdb=" SG CYS B 804 " pdb="FE1 SF4 B1102 " - pdb=" SG CYS B 934 " pdb="FE2 SF4 B1102 " - pdb=" SG CYS B 931 " pdb="FE4 SF4 B1102 " - pdb=" SG CYS B 968 " pdb=" SF4 B1103 " pdb="FE3 SF4 B1103 " - pdb=" SG CYS B 892 " pdb="FE1 SF4 B1103 " - pdb=" SG CYS B 850 " pdb="FE4 SF4 B1103 " - pdb=" SG CYS B 853 " pdb="FE2 SF4 B1103 " - pdb=" SG CYS B 858 " Number of angles added : 45 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4564 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 14 sheets defined 47.5% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 7 through 35 removed outlier: 4.189A pdb=" N ASN A 10 " --> pdb=" O ARG A 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 15 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 18 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 32 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 58 No H-bonds generated for 'chain 'A' and resid 55 through 58' Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 84 through 91 removed outlier: 4.598A pdb=" N CYS A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 106 removed outlier: 3.796A pdb=" N GLU A 102 " --> pdb=" O PRO A 99 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LYS A 103 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 161 through 169 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 192 through 203 Processing helix chain 'A' and resid 208 through 211 No H-bonds generated for 'chain 'A' and resid 208 through 211' Processing helix chain 'A' and resid 214 through 217 No H-bonds generated for 'chain 'A' and resid 214 through 217' Processing helix chain 'B' and resid 142 through 151 removed outlier: 4.723A pdb=" N ILE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU B 149 " --> pdb=" O GLN B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 184 Processing helix chain 'B' and resid 201 through 213 Processing helix chain 'B' and resid 228 through 238 Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 268 through 279 Processing helix chain 'B' and resid 300 through 304 removed outlier: 4.016A pdb=" N ALA B 304 " --> pdb=" O THR B 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 300 through 304' Processing helix chain 'B' and resid 313 through 327 removed outlier: 3.758A pdb=" N ILE B 316 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA B 317 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 327 " --> pdb=" O ALA B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'B' and resid 368 through 380 Processing helix chain 'B' and resid 401 through 413 Processing helix chain 'B' and resid 427 through 430 No H-bonds generated for 'chain 'B' and resid 427 through 430' Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 456 through 460 removed outlier: 3.607A pdb=" N ARG B 460 " --> pdb=" O GLU B 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 456 through 460' Processing helix chain 'B' and resid 470 through 472 No H-bonds generated for 'chain 'B' and resid 470 through 472' Processing helix chain 'B' and resid 500 through 508 Processing helix chain 'B' and resid 515 through 523 Processing helix chain 'B' and resid 529 through 537 removed outlier: 3.608A pdb=" N VAL B 534 " --> pdb=" O THR B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 559 removed outlier: 3.528A pdb=" N ARG B 559 " --> pdb=" O GLU B 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 555 through 559' Processing helix chain 'B' and resid 584 through 587 removed outlier: 4.437A pdb=" N ASN B 587 " --> pdb=" O PHE B 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 584 through 587' Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 611 through 617 Processing helix chain 'B' and resid 631 through 644 removed outlier: 6.331A pdb=" N ARG B 635 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU B 636 " --> pdb=" O ASP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 701 No H-bonds generated for 'chain 'B' and resid 699 through 701' Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 751 through 762 removed outlier: 4.381A pdb=" N ILE B 754 " --> pdb=" O PRO B 751 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B 757 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR B 759 " --> pdb=" O LYS B 756 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN B 760 " --> pdb=" O GLU B 757 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU B 762 " --> pdb=" O TYR B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 807 Processing helix chain 'B' and resid 815 through 820 Processing helix chain 'B' and resid 887 through 891 Processing helix chain 'B' and resid 910 through 914 Processing helix chain 'B' and resid 935 through 952 Processing helix chain 'B' and resid 967 through 970 No H-bonds generated for 'chain 'B' and resid 967 through 970' Processing helix chain 'B' and resid 988 through 993 Processing helix chain 'C' and resid 25 through 33 Processing helix chain 'C' and resid 45 through 71 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 86 through 110 removed outlier: 4.051A pdb=" N GLY C 98 " --> pdb=" O TRP C 94 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N HIS C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY C 101 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 140 removed outlier: 3.820A pdb=" N LEU C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR C 137 " --> pdb=" O CYS C 133 " (cutoff:3.500A) Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 145 through 151 removed outlier: 4.830A pdb=" N TYR C 149 " --> pdb=" O TRP C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 199 removed outlier: 3.888A pdb=" N PHE C 173 " --> pdb=" O ALA C 169 " (cutoff:3.500A) Proline residue: C 192 - end of helix Processing helix chain 'C' and resid 204 through 214 removed outlier: 3.628A pdb=" N ARG C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 254 Proline residue: C 240 - end of helix removed outlier: 3.868A pdb=" N VAL C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE C 253 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 291 Proline residue: C 288 - end of helix Processing helix chain 'C' and resid 301 through 331 Processing helix chain 'C' and resid 335 through 346 Processing helix chain 'C' and resid 350 through 359 Processing helix chain 'C' and resid 365 through 368 removed outlier: 3.580A pdb=" N TRP C 368 " --> pdb=" O GLN C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 368' Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 376 through 403 removed outlier: 3.962A pdb=" N ILE C 400 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 418 through 441 Processing helix chain 'C' and resid 451 through 463 Processing helix chain 'D' and resid 15 through 24 Processing helix chain 'D' and resid 44 through 47 No H-bonds generated for 'chain 'D' and resid 44 through 47' Processing helix chain 'D' and resid 55 through 79 Processing helix chain 'D' and resid 93 through 95 No H-bonds generated for 'chain 'D' and resid 93 through 95' Processing helix chain 'D' and resid 100 through 122 Processing helix chain 'D' and resid 131 through 134 Processing helix chain 'D' and resid 138 through 140 No H-bonds generated for 'chain 'D' and resid 138 through 140' Processing helix chain 'D' and resid 159 through 168 Processing helix chain 'E' and resid 68 through 71 No H-bonds generated for 'chain 'E' and resid 68 through 71' Processing helix chain 'E' and resid 89 through 102 Processing helix chain 'E' and resid 131 through 134 No H-bonds generated for 'chain 'E' and resid 131 through 134' Processing helix chain 'E' and resid 138 through 147 Processing helix chain 'E' and resid 171 through 188 Processing helix chain 'F' and resid 12 through 38 Processing helix chain 'F' and resid 40 through 70 removed outlier: 4.749A pdb=" N ILE F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) Proline residue: F 58 - end of helix Processing helix chain 'F' and resid 74 through 78 Processing helix chain 'F' and resid 80 through 88 Processing helix chain 'F' and resid 90 through 104 Proline residue: F 99 - end of helix Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'F' and resid 146 through 175 removed outlier: 3.898A pdb=" N ASP F 175 " --> pdb=" O SER F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 210 removed outlier: 4.097A pdb=" N ALA F 196 " --> pdb=" O GLY F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 244 removed outlier: 3.712A pdb=" N ARG F 244 " --> pdb=" O LEU F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 254 Processing helix chain 'F' and resid 257 through 287 Processing helix chain 'F' and resid 294 through 298 Processing helix chain 'F' and resid 305 through 315 Processing helix chain 'F' and resid 318 through 325 Processing helix chain 'F' and resid 334 through 358 Proline residue: F 357 - end of helix Processing helix chain 'F' and resid 368 through 390 removed outlier: 5.141A pdb=" N ALA F 373 " --> pdb=" O ASP F 370 " (cutoff:3.500A) Proline residue: F 374 - end of helix removed outlier: 3.517A pdb=" N LEU F 377 " --> pdb=" O PRO F 374 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE F 378 " --> pdb=" O ILE F 375 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL F 389 " --> pdb=" O ALA F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 404 No H-bonds generated for 'chain 'F' and resid 402 through 404' Processing helix chain 'G' and resid 34 through 55 Processing helix chain 'G' and resid 70 through 81 Processing helix chain 'G' and resid 99 through 106 Processing helix chain 'I' and resid 9 through 34 removed outlier: 3.862A pdb=" N LYS I 12 " --> pdb=" O PRO I 9 " (cutoff:3.500A) Proline residue: I 13 - end of helix removed outlier: 3.522A pdb=" N LEU I 16 " --> pdb=" O PRO I 13 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL I 18 " --> pdb=" O PHE I 15 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET I 23 " --> pdb=" O LEU I 20 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA I 25 " --> pdb=" O GLY I 22 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N PHE I 26 " --> pdb=" O MET I 23 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU I 27 " --> pdb=" O VAL I 24 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU I 32 " --> pdb=" O MET I 29 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE I 33 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA I 34 " --> pdb=" O TRP I 31 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 100 through 107 removed outlier: 3.932A pdb=" N LYS B 126 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 191 through 195 removed outlier: 5.940A pdb=" N THR B 419 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU B 194 " --> pdb=" O THR B 419 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE B 421 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU B 446 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N MET B 422 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE B 448 " --> pdb=" O MET B 422 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 242 through 246 Processing sheet with id= D, first strand: chain 'B' and resid 358 through 362 removed outlier: 6.332A pdb=" N VAL B 253 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE B 361 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL B 255 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ARG B 290 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N SER B 256 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TYR B 292 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N HIS B 307 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLU B 295 " --> pdb=" O HIS B 307 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU B 309 " --> pdb=" O GLU B 295 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 475 through 477 Processing sheet with id= F, first strand: chain 'B' and resid 571 through 576 Processing sheet with id= G, first strand: chain 'B' and resid 607 through 609 Processing sheet with id= H, first strand: chain 'B' and resid 741 through 743 removed outlier: 6.809A pdb=" N ARG B1016 " --> pdb=" O GLY B 742 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 977 through 981 Processing sheet with id= J, first strand: chain 'B' and resid 828 through 831 Processing sheet with id= K, first strand: chain 'B' and resid 867 through 869 Processing sheet with id= L, first strand: chain 'B' and resid 651 through 653 removed outlier: 3.530A pdb=" N ILE B 651 " --> pdb=" O GLY B 719 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY B 719 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ARG B 653 " --> pdb=" O ASN B 717 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASN B 717 " --> pdb=" O ARG B 653 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 7 through 9 Processing sheet with id= N, first strand: chain 'D' and resid 33 through 36 767 hydrogen bonds defined for protein. 2052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.34 Time building geometry restraints manager: 9.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.71: 20269 1.71 - 2.25: 201 2.25 - 2.79: 30 2.79 - 3.33: 0 3.33 - 3.87: 3 Bond restraints: 20503 Sorted by residual: bond pdb=" S1 F3S B1104 " pdb="FE4 F3S B1104 " ideal model delta sigma weight residual 2.258 3.867 -1.609 2.00e-02 2.50e+03 6.47e+03 bond pdb=" S4 F3S B1104 " pdb="FE1 F3S B1104 " ideal model delta sigma weight residual 2.233 3.778 -1.545 2.00e-02 2.50e+03 5.97e+03 bond pdb=" S2 F3S B1104 " pdb="FE3 F3S B1104 " ideal model delta sigma weight residual 2.300 3.676 -1.376 2.00e-02 2.50e+03 4.74e+03 bond pdb=" C15 JM9 F 502 " pdb=" O16 JM9 F 502 " ideal model delta sigma weight residual 1.183 1.314 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" C2A HEC A 302 " pdb=" C3A HEC A 302 " ideal model delta sigma weight residual 1.334 1.439 -0.105 2.00e-02 2.50e+03 2.78e+01 ... (remaining 20498 not shown) Histogram of bond angle deviations from ideal: 36.92 - 65.14: 4 65.14 - 93.36: 62 93.36 - 121.58: 23166 121.58 - 149.80: 4805 149.80 - 178.02: 12 Bond angle restraints: 28049 Sorted by residual: angle pdb=" S3 F3S B1104 " pdb="FE1 F3S B1104 " pdb=" S4 F3S B1104 " ideal model delta sigma weight residual 112.59 66.57 46.02 3.00e+00 1.11e-01 2.35e+02 angle pdb=" S1 F3S B1104 " pdb="FE4 F3S B1104 " pdb=" S3 F3S B1104 " ideal model delta sigma weight residual 114.75 69.63 45.12 3.00e+00 1.11e-01 2.26e+02 angle pdb=" S1 F3S B1104 " pdb="FE4 F3S B1104 " pdb=" S2 F3S B1104 " ideal model delta sigma weight residual 103.63 65.14 38.49 3.00e+00 1.11e-01 1.65e+02 angle pdb="FE1 F3S B1104 " pdb=" S4 F3S B1104 " pdb="FE3 F3S B1104 " ideal model delta sigma weight residual 74.86 36.92 37.94 3.00e+00 1.11e-01 1.60e+02 angle pdb=" S1 F3S B1104 " pdb="FE3 F3S B1104 " pdb=" S2 F3S B1104 " ideal model delta sigma weight residual 103.25 69.11 34.14 3.00e+00 1.11e-01 1.29e+02 ... (remaining 28044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.38: 11191 32.38 - 64.76: 574 64.76 - 97.15: 66 97.15 - 129.53: 7 129.53 - 161.91: 4 Dihedral angle restraints: 11842 sinusoidal: 4704 harmonic: 7138 Sorted by residual: dihedral pdb=" C2C HEC A 303 " pdb=" C3C HEC A 303 " pdb=" CAC HEC A 303 " pdb=" CBC HEC A 303 " ideal model delta sinusoidal sigma weight residual 240.00 152.70 87.30 2 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CA LYS A 95 " pdb=" C LYS A 95 " pdb=" N THR A 96 " pdb=" CA THR A 96 " ideal model delta harmonic sigma weight residual 180.00 150.19 29.81 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA GLY C 143 " pdb=" C GLY C 143 " pdb=" N ARG C 144 " pdb=" CA ARG C 144 " ideal model delta harmonic sigma weight residual 180.00 150.45 29.55 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 11839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.568: 3043 3.568 - 7.136: 0 7.136 - 10.704: 0 10.704 - 14.273: 0 14.273 - 17.841: 1 Chirality restraints: 3044 Sorted by residual: chirality pdb=" S2 F3S B1104 " pdb="FE1 F3S B1104 " pdb="FE3 F3S B1104 " pdb="FE4 F3S B1104 " both_signs ideal model delta sigma weight residual False 10.77 -7.07 17.84 2.00e-01 2.50e+01 7.96e+03 chirality pdb=" CA LEU D 125 " pdb=" N LEU D 125 " pdb=" C LEU D 125 " pdb=" CB LEU D 125 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.55e+01 chirality pdb=" CA TYR B 957 " pdb=" N TYR B 957 " pdb=" C TYR B 957 " pdb=" CB TYR B 957 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.51e+00 ... (remaining 3041 not shown) Planarity restraints: 3537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A HEC A 302 " -0.033 2.00e-02 2.50e+03 1.03e-01 2.39e+02 pdb=" C2A HEC A 302 " 0.026 2.00e-02 2.50e+03 pdb=" C3A HEC A 302 " -0.104 2.00e-02 2.50e+03 pdb=" C4A HEC A 302 " 0.042 2.00e-02 2.50e+03 pdb=" CAA HEC A 302 " 0.185 2.00e-02 2.50e+03 pdb=" CHA HEC A 302 " -0.112 2.00e-02 2.50e+03 pdb=" CHB HEC A 302 " 0.119 2.00e-02 2.50e+03 pdb=" CMA HEC A 302 " -0.141 2.00e-02 2.50e+03 pdb=" NA HEC A 302 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A 303 " 0.055 2.00e-02 2.50e+03 8.43e-02 1.60e+02 pdb=" C2C HEC A 303 " -0.229 2.00e-02 2.50e+03 pdb=" C3C HEC A 303 " 0.016 2.00e-02 2.50e+03 pdb=" C4C HEC A 303 " 0.019 2.00e-02 2.50e+03 pdb=" CAC HEC A 303 " 0.058 2.00e-02 2.50e+03 pdb=" CHC HEC A 303 " 0.041 2.00e-02 2.50e+03 pdb=" CHD HEC A 303 " -0.008 2.00e-02 2.50e+03 pdb=" CMC HEC A 303 " 0.052 2.00e-02 2.50e+03 pdb=" NC HEC A 303 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A 302 " -0.021 2.00e-02 2.50e+03 8.00e-02 1.44e+02 pdb=" C2C HEC A 302 " 0.217 2.00e-02 2.50e+03 pdb=" C3C HEC A 302 " -0.014 2.00e-02 2.50e+03 pdb=" C4C HEC A 302 " 0.002 2.00e-02 2.50e+03 pdb=" CAC HEC A 302 " -0.052 2.00e-02 2.50e+03 pdb=" CHC HEC A 302 " -0.053 2.00e-02 2.50e+03 pdb=" CHD HEC A 302 " -0.011 2.00e-02 2.50e+03 pdb=" CMC HEC A 302 " -0.066 2.00e-02 2.50e+03 pdb=" NC HEC A 302 " -0.000 2.00e-02 2.50e+03 ... (remaining 3534 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 209 2.57 - 3.16: 15852 3.16 - 3.74: 34755 3.74 - 4.32: 48883 4.32 - 4.90: 77701 Nonbonded interactions: 177400 Sorted by model distance: nonbonded pdb=" OE1 GLN B 82 " pdb="MG MG B1105 " model vdw 1.993 2.170 nonbonded pdb=" OD1 ASP E 32 " pdb="MG MG B1105 " model vdw 2.058 2.170 nonbonded pdb=" NE2 HIS A 70 " pdb="FE HEC A 304 " model vdw 2.077 3.080 nonbonded pdb=" NE2 HIS A 218 " pdb="FE HEC A 301 " model vdw 2.083 3.080 nonbonded pdb=" NE2 GLN B 79 " pdb="MG MG B1105 " model vdw 2.091 2.250 ... (remaining 177395 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 3.460 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 58.480 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 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:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 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 : 0.021 1.609 20503 Z= 1.413 Angle : 1.528 46.023 28049 Z= 0.714 Chirality : 0.331 17.841 3044 Planarity : 0.011 0.103 3537 Dihedral : 19.337 161.912 7278 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.13 % Allowed : 27.86 % Favored : 69.01 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.14), residues: 2455 helix: -1.77 (0.12), residues: 1251 sheet: -1.68 (0.38), residues: 169 loop : -1.98 (0.17), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP C 421 HIS 0.032 0.004 HIS C 246 PHE 0.070 0.004 PHE F 218 TYR 0.049 0.003 TYR C 424 ARG 0.016 0.001 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 458 time to evaluate : 2.287 Fit side-chains REVERT: B 191 VAL cc_start: 0.8327 (p) cc_final: 0.8062 (m) REVERT: B 582 ASP cc_start: 0.6622 (p0) cc_final: 0.6182 (p0) REVERT: C 190 LEU cc_start: 0.6996 (tp) cc_final: 0.6740 (tp) REVERT: C 296 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.5851 (mt-10) outliers start: 64 outliers final: 44 residues processed: 503 average time/residue: 1.0742 time to fit residues: 626.3513 Evaluate side-chains 438 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 393 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 729 ASP Chi-restraints excluded: chain B residue 752 LYS Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 931 CYS Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 448 PHE Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 74 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 6.9990 chunk 184 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 220 optimal weight: 0.5980 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 HIS B 209 GLN B 365 GLN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS B 876 ASN B 965 GLN B1019 ASN C 163 GLN C 463 GLN D 50 HIS E 78 GLN E 130 GLN E 140 HIS E 188 GLN ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN G 68 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 20503 Z= 0.213 Angle : 0.918 88.858 28049 Z= 0.381 Chirality : 0.047 1.186 3044 Planarity : 0.006 0.075 3537 Dihedral : 13.822 178.032 2943 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 5.96 % Allowed : 27.52 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.16), residues: 2455 helix: -0.65 (0.13), residues: 1251 sheet: -1.39 (0.39), residues: 160 loop : -1.60 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 274 HIS 0.005 0.001 HIS C 246 PHE 0.036 0.001 PHE F 237 TYR 0.017 0.001 TYR C 227 ARG 0.007 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 436 time to evaluate : 2.076 Fit side-chains REVERT: A 14 ARG cc_start: 0.6759 (mpt180) cc_final: 0.6558 (mpt180) REVERT: A 74 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7503 (p0) REVERT: B 90 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6826 (mt0) REVERT: B 345 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6635 (mtt-85) REVERT: B 365 GLN cc_start: 0.6391 (OUTLIER) cc_final: 0.6076 (pt0) REVERT: B 397 ARG cc_start: 0.5560 (OUTLIER) cc_final: 0.5181 (ttp-170) REVERT: B 549 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7382 (pp) REVERT: B 582 ASP cc_start: 0.6726 (p0) cc_final: 0.6193 (p0) REVERT: B 593 GLU cc_start: 0.8283 (tp30) cc_final: 0.8007 (tp30) REVERT: B 838 LEU cc_start: 0.7098 (mt) cc_final: 0.6631 (mt) REVERT: B 954 GLN cc_start: 0.6472 (mt0) cc_final: 0.6230 (tm130) REVERT: B 957 TYR cc_start: 0.7294 (t80) cc_final: 0.6428 (t80) REVERT: C 55 PHE cc_start: 0.6743 (OUTLIER) cc_final: 0.6375 (t80) REVERT: C 208 ARG cc_start: 0.6447 (mmt90) cc_final: 0.6095 (mpt-90) REVERT: C 460 LYS cc_start: 0.6162 (tptt) cc_final: 0.5891 (ttmm) REVERT: D 89 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.5153 (mmt90) REVERT: F 104 TYR cc_start: 0.7012 (p90) cc_final: 0.6642 (p90) REVERT: F 152 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.6126 (mtp85) REVERT: F 188 ARG cc_start: 0.6684 (ttp80) cc_final: 0.6407 (ttp80) REVERT: F 397 LEU cc_start: 0.5593 (OUTLIER) cc_final: 0.5296 (pp) REVERT: G 32 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6160 (tt) REVERT: G 111 ARG cc_start: 0.6197 (OUTLIER) cc_final: 0.5993 (mtp85) outliers start: 122 outliers final: 51 residues processed: 509 average time/residue: 1.0418 time to fit residues: 617.8298 Evaluate side-chains 463 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 400 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 345 ARG Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 1014 LEU Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 152 ARG Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 111 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 7.9990 chunk 68 optimal weight: 40.0000 chunk 183 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 238 optimal weight: 0.0980 chunk 196 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 177 optimal weight: 10.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 91 HIS B 206 GLN B 209 GLN B 501 ASN B 587 ASN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS B 876 ASN B 965 GLN B1019 ASN C 365 GLN ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN F 122 ASN F 388 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 20503 Z= 0.264 Angle : 0.911 83.335 28049 Z= 0.378 Chirality : 0.051 1.462 3044 Planarity : 0.006 0.069 3537 Dihedral : 12.735 150.347 2898 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 7.77 % Allowed : 27.32 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.16), residues: 2455 helix: -0.30 (0.14), residues: 1258 sheet: -1.44 (0.38), residues: 176 loop : -1.34 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 274 HIS 0.006 0.001 HIS A 70 PHE 0.024 0.002 PHE D 138 TYR 0.015 0.002 TYR F 279 ARG 0.009 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 428 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6605 (mpt180) cc_final: 0.6349 (mpt180) REVERT: A 130 HIS cc_start: 0.9248 (OUTLIER) cc_final: 0.8959 (m-70) REVERT: B 90 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.6855 (mt0) REVERT: B 163 GLN cc_start: 0.6555 (OUTLIER) cc_final: 0.6222 (mt0) REVERT: B 176 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7616 (tm) REVERT: B 397 ARG cc_start: 0.5640 (OUTLIER) cc_final: 0.5280 (ttp-170) REVERT: B 549 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7483 (pp) REVERT: B 593 GLU cc_start: 0.8321 (tp30) cc_final: 0.8039 (tp30) REVERT: B 596 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7931 (mtt90) REVERT: B 838 LEU cc_start: 0.7074 (mt) cc_final: 0.6600 (mt) REVERT: C 55 PHE cc_start: 0.6876 (OUTLIER) cc_final: 0.6627 (t80) REVERT: C 183 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8012 (tm) REVERT: C 208 ARG cc_start: 0.6637 (mmt90) cc_final: 0.5974 (mpt180) REVERT: C 316 MET cc_start: 0.8232 (mmm) cc_final: 0.7724 (mmp) REVERT: C 444 MET cc_start: 0.7361 (ptp) cc_final: 0.6938 (mpp) REVERT: D 89 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.6790 (mmt90) REVERT: D 102 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.8003 (mt) REVERT: F 188 ARG cc_start: 0.6626 (ttp80) cc_final: 0.6324 (ttp80) REVERT: F 211 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7361 (ttp) REVERT: F 371 VAL cc_start: 0.7457 (t) cc_final: 0.6903 (p) REVERT: F 397 LEU cc_start: 0.5891 (OUTLIER) cc_final: 0.5602 (pp) REVERT: G 111 ARG cc_start: 0.6373 (OUTLIER) cc_final: 0.6013 (mtp85) REVERT: I 12 LYS cc_start: 0.5470 (OUTLIER) cc_final: 0.4732 (tmmt) outliers start: 159 outliers final: 83 residues processed: 529 average time/residue: 1.0509 time to fit residues: 650.2787 Evaluate side-chains 491 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 393 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 187 GLN Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 596 ARG Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 152 ARG Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain I residue 12 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 20.0000 chunk 166 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 234 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 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 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS B 954 GLN B1019 ASN C 343 ASN C 463 GLN D 50 HIS ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** F 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 20503 Z= 0.254 Angle : 0.890 82.702 28049 Z= 0.370 Chirality : 0.051 1.504 3044 Planarity : 0.005 0.071 3537 Dihedral : 12.196 151.269 2893 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 8.16 % Allowed : 27.76 % Favored : 64.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.17), residues: 2455 helix: -0.07 (0.14), residues: 1248 sheet: -1.39 (0.39), residues: 175 loop : -1.25 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 274 HIS 0.006 0.001 HIS D 130 PHE 0.027 0.001 PHE F 237 TYR 0.016 0.002 TYR B 957 ARG 0.010 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 418 time to evaluate : 2.225 Fit side-chains revert: symmetry clash REVERT: A 65 ASP cc_start: 0.7668 (t70) cc_final: 0.7104 (t70) REVERT: A 74 ASP cc_start: 0.7999 (p0) cc_final: 0.7777 (p0) REVERT: A 130 HIS cc_start: 0.9203 (OUTLIER) cc_final: 0.8896 (m90) REVERT: B 90 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.6877 (mt0) REVERT: B 163 GLN cc_start: 0.6516 (OUTLIER) cc_final: 0.6146 (mt0) REVERT: B 397 ARG cc_start: 0.5675 (OUTLIER) cc_final: 0.5314 (ttp-170) REVERT: B 596 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7945 (mtt90) REVERT: B 838 LEU cc_start: 0.7017 (mt) cc_final: 0.6525 (mt) REVERT: B 957 TYR cc_start: 0.7231 (t80) cc_final: 0.6141 (t80) REVERT: C 55 PHE cc_start: 0.6932 (OUTLIER) cc_final: 0.6704 (t80) REVERT: C 183 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8008 (tm) REVERT: C 208 ARG cc_start: 0.6689 (mmt90) cc_final: 0.6337 (mmt90) REVERT: C 385 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7575 (mp) REVERT: D 89 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7192 (mmt90) REVERT: D 102 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.8027 (mt) REVERT: F 188 ARG cc_start: 0.6532 (ttp80) cc_final: 0.6241 (ttp80) REVERT: F 211 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7337 (ttp) REVERT: F 371 VAL cc_start: 0.7422 (t) cc_final: 0.6913 (p) REVERT: G 34 ARG cc_start: 0.5314 (OUTLIER) cc_final: 0.4496 (ptm160) REVERT: G 55 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6105 (mpt90) REVERT: G 111 ARG cc_start: 0.6343 (OUTLIER) cc_final: 0.5950 (mmp80) REVERT: I 12 LYS cc_start: 0.5551 (OUTLIER) cc_final: 0.4774 (tmmt) REVERT: I 29 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6112 (mtt) outliers start: 167 outliers final: 85 residues processed: 529 average time/residue: 1.0325 time to fit residues: 637.7876 Evaluate side-chains 500 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 399 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 596 ARG Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 974 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 152 ARG Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 29 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 6.9990 chunk 133 optimal weight: 0.0980 chunk 3 optimal weight: 8.9990 chunk 174 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 119 optimal weight: 7.9990 chunk 210 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 HIS ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN B1019 ASN C 343 ASN ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS D 95 ASN E 140 HIS E 188 GLN F 388 ASN ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 20503 Z= 0.369 Angle : 0.962 83.215 28049 Z= 0.404 Chirality : 0.054 1.475 3044 Planarity : 0.006 0.072 3537 Dihedral : 12.150 144.551 2891 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 8.55 % Allowed : 26.93 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.16), residues: 2455 helix: -0.21 (0.14), residues: 1244 sheet: -1.47 (0.38), residues: 176 loop : -1.22 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 274 HIS 0.008 0.002 HIS D 130 PHE 0.036 0.002 PHE F 237 TYR 0.020 0.002 TYR F 108 ARG 0.012 0.001 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 420 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 HIS cc_start: 0.9261 (OUTLIER) cc_final: 0.8979 (m-70) REVERT: B 90 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7025 (mt0) REVERT: B 163 GLN cc_start: 0.6643 (OUTLIER) cc_final: 0.6295 (mt0) REVERT: B 176 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7600 (tm) REVERT: B 397 ARG cc_start: 0.5644 (OUTLIER) cc_final: 0.5336 (ttp-170) REVERT: B 549 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7197 (pp) REVERT: B 596 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7981 (mtt90) REVERT: B 765 ARG cc_start: 0.7369 (mtm110) cc_final: 0.6773 (ptp-110) REVERT: C 55 PHE cc_start: 0.6971 (OUTLIER) cc_final: 0.6742 (t80) REVERT: C 183 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8004 (tm) REVERT: C 444 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7155 (mpp) REVERT: D 102 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7994 (mt) REVERT: F 211 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7374 (ttp) REVERT: F 253 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.6165 (tp30) REVERT: F 371 VAL cc_start: 0.7480 (t) cc_final: 0.6989 (p) REVERT: G 34 ARG cc_start: 0.5313 (OUTLIER) cc_final: 0.4487 (ptm160) REVERT: G 55 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6290 (mpt90) REVERT: G 105 GLU cc_start: 0.6149 (OUTLIER) cc_final: 0.5812 (tp30) REVERT: G 111 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.6067 (mmp80) REVERT: I 12 LYS cc_start: 0.5732 (OUTLIER) cc_final: 0.4927 (tmmt) REVERT: I 29 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.6159 (mtt) outliers start: 175 outliers final: 103 residues processed: 538 average time/residue: 1.0653 time to fit residues: 673.6165 Evaluate side-chains 524 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 402 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 365 GLN Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 596 ARG Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 974 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 87 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 152 ARG Chi-restraints excluded: chain F residue 211 MET Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 253 GLU Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 29 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 0.9980 chunk 211 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 235 optimal weight: 0.9990 chunk 195 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 187 GLN B 209 GLN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS ** B 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN B1019 ASN C 343 ASN ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS E 188 GLN F 388 ASN F 390 GLN ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 20503 Z= 0.251 Angle : 0.896 82.389 28049 Z= 0.373 Chirality : 0.051 1.500 3044 Planarity : 0.005 0.071 3537 Dihedral : 11.710 146.610 2891 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 7.33 % Allowed : 28.79 % Favored : 63.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2455 helix: 0.01 (0.14), residues: 1238 sheet: -1.23 (0.40), residues: 168 loop : -1.19 (0.20), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 274 HIS 0.006 0.001 HIS C 246 PHE 0.028 0.001 PHE D 138 TYR 0.022 0.002 TYR E 71 ARG 0.013 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 420 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.7689 (t70) cc_final: 0.7127 (t70) REVERT: B 90 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6964 (mt0) REVERT: B 163 GLN cc_start: 0.6501 (OUTLIER) cc_final: 0.6180 (mt0) REVERT: B 176 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7746 (tm) REVERT: B 191 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8116 (m) REVERT: B 212 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7534 (tp40) REVERT: B 397 ARG cc_start: 0.5743 (OUTLIER) cc_final: 0.5498 (ttp-170) REVERT: B 549 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7260 (pp) REVERT: B 596 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7986 (mtt90) REVERT: B 765 ARG cc_start: 0.7305 (mtm110) cc_final: 0.6783 (ptp-110) REVERT: C 55 PHE cc_start: 0.7001 (OUTLIER) cc_final: 0.6766 (t80) REVERT: C 183 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7974 (tm) REVERT: C 229 MET cc_start: 0.7436 (tpp) cc_final: 0.7188 (tpp) REVERT: C 323 PHE cc_start: 0.6989 (OUTLIER) cc_final: 0.6664 (m-80) REVERT: C 444 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7096 (mpp) REVERT: D 89 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7673 (mmt90) REVERT: E 71 TYR cc_start: 0.6545 (m-10) cc_final: 0.6243 (m-10) REVERT: F 371 VAL cc_start: 0.7342 (t) cc_final: 0.6912 (p) REVERT: G 34 ARG cc_start: 0.5266 (mtt90) cc_final: 0.4550 (ptm160) REVERT: G 55 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6111 (mpt90) REVERT: G 111 ARG cc_start: 0.6274 (OUTLIER) cc_final: 0.5931 (mmp80) REVERT: I 12 LYS cc_start: 0.5704 (OUTLIER) cc_final: 0.4897 (tmmt) REVERT: I 29 MET cc_start: 0.6771 (OUTLIER) cc_final: 0.6125 (mtt) outliers start: 150 outliers final: 86 residues processed: 519 average time/residue: 1.0605 time to fit residues: 642.4694 Evaluate side-chains 495 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 392 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 596 ARG Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 929 GLU Chi-restraints excluded: chain B residue 974 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 152 ARG Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 29 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 234 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 GLN B 357 GLN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS B 876 ASN B 891 ASN B 954 GLN B1019 ASN ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS E 140 HIS F 388 ASN F 390 GLN ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 20503 Z= 0.252 Angle : 0.896 82.661 28049 Z= 0.373 Chirality : 0.051 1.493 3044 Planarity : 0.005 0.067 3537 Dihedral : 11.438 147.044 2889 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 7.04 % Allowed : 29.57 % Favored : 63.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.17), residues: 2455 helix: 0.12 (0.14), residues: 1241 sheet: -1.17 (0.40), residues: 168 loop : -1.18 (0.20), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 274 HIS 0.005 0.001 HIS D 130 PHE 0.029 0.001 PHE D 138 TYR 0.024 0.002 TYR F 108 ARG 0.011 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 414 time to evaluate : 2.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.7660 (t70) cc_final: 0.7104 (t70) REVERT: A 180 GLU cc_start: 0.5555 (pm20) cc_final: 0.5337 (pm20) REVERT: B 90 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.6970 (mt0) REVERT: B 145 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7880 (mp10) REVERT: B 163 GLN cc_start: 0.6506 (OUTLIER) cc_final: 0.6181 (mt0) REVERT: B 176 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7740 (tm) REVERT: B 191 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8104 (m) REVERT: B 218 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.6909 (mtp85) REVERT: B 299 SER cc_start: 0.7427 (p) cc_final: 0.7057 (t) REVERT: B 345 ARG cc_start: 0.6878 (mtt-85) cc_final: 0.6674 (mpp80) REVERT: B 397 ARG cc_start: 0.5748 (OUTLIER) cc_final: 0.5486 (ttp-170) REVERT: B 593 GLU cc_start: 0.8333 (tp30) cc_final: 0.8024 (tp30) REVERT: B 596 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7973 (mtt90) REVERT: B 838 LEU cc_start: 0.7076 (mt) cc_final: 0.6543 (mt) REVERT: C 55 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6768 (t80) REVERT: C 183 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7984 (tm) REVERT: C 229 MET cc_start: 0.7463 (tpp) cc_final: 0.7192 (tpp) REVERT: C 323 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.6643 (m-80) REVERT: C 444 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.7119 (mpp) REVERT: D 89 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.6913 (mmt90) REVERT: E 71 TYR cc_start: 0.6563 (m-10) cc_final: 0.6192 (m-10) REVERT: F 253 GLU cc_start: 0.6374 (tp30) cc_final: 0.5907 (tp30) REVERT: F 371 VAL cc_start: 0.7309 (t) cc_final: 0.6969 (p) REVERT: F 397 LEU cc_start: 0.5826 (OUTLIER) cc_final: 0.5573 (pp) REVERT: G 32 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6070 (tt) REVERT: G 55 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6106 (mpt90) REVERT: G 111 ARG cc_start: 0.6283 (OUTLIER) cc_final: 0.5925 (mmp80) REVERT: I 12 LYS cc_start: 0.5712 (OUTLIER) cc_final: 0.4911 (tmmt) REVERT: I 29 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6039 (mtt) outliers start: 144 outliers final: 95 residues processed: 510 average time/residue: 1.1133 time to fit residues: 668.7055 Evaluate side-chains 514 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 400 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 397 ARG Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 596 ARG Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 929 GLU Chi-restraints excluded: chain B residue 974 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 152 ARG Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 242 MET Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 334 ASN Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 29 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 148 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 21 optimal weight: 0.0370 chunk 184 optimal weight: 3.9990 chunk 213 optimal weight: 10.0000 overall best weight: 2.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 187 GLN B 226 ASN B 357 GLN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS B 954 GLN B1019 ASN C 463 GLN D 50 HIS ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 GLN F 388 ASN F 390 GLN ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 20503 Z= 0.242 Angle : 0.890 82.530 28049 Z= 0.371 Chirality : 0.051 1.504 3044 Planarity : 0.005 0.068 3537 Dihedral : 11.231 147.436 2889 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 6.50 % Allowed : 30.21 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.73 (0.17), residues: 2455 helix: 0.24 (0.14), residues: 1223 sheet: -1.06 (0.42), residues: 155 loop : -1.17 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP F 274 HIS 0.005 0.001 HIS D 130 PHE 0.029 0.001 PHE D 138 TYR 0.022 0.001 TYR F 36 ARG 0.013 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 417 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.7658 (t70) cc_final: 0.7105 (t70) REVERT: A 180 GLU cc_start: 0.5520 (pm20) cc_final: 0.5302 (pm20) REVERT: B 90 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.6966 (mt0) REVERT: B 145 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: B 163 GLN cc_start: 0.6529 (OUTLIER) cc_final: 0.6186 (mt0) REVERT: B 176 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7739 (tm) REVERT: B 184 ARG cc_start: 0.6608 (ttm110) cc_final: 0.6297 (ttm110) REVERT: B 191 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8099 (m) REVERT: B 218 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.6927 (mtp85) REVERT: B 299 SER cc_start: 0.7457 (p) cc_final: 0.7116 (t) REVERT: B 345 ARG cc_start: 0.6574 (mtt-85) cc_final: 0.6366 (mpp80) REVERT: B 593 GLU cc_start: 0.8340 (tp30) cc_final: 0.8001 (tp30) REVERT: B 596 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7963 (mtt90) REVERT: B 765 ARG cc_start: 0.7312 (mtm110) cc_final: 0.6703 (ptp-110) REVERT: B 838 LEU cc_start: 0.7012 (mt) cc_final: 0.6523 (mt) REVERT: C 55 PHE cc_start: 0.7031 (OUTLIER) cc_final: 0.6778 (t80) REVERT: C 183 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7972 (tm) REVERT: C 229 MET cc_start: 0.7468 (tpp) cc_final: 0.7200 (tpp) REVERT: C 323 PHE cc_start: 0.6952 (OUTLIER) cc_final: 0.6624 (m-80) REVERT: C 444 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7116 (mpp) REVERT: C 448 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.6953 (p90) REVERT: D 89 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.5609 (mmt90) REVERT: E 71 TYR cc_start: 0.6524 (m-10) cc_final: 0.6063 (m-10) REVERT: F 253 GLU cc_start: 0.6234 (tp30) cc_final: 0.5844 (tp30) REVERT: F 371 VAL cc_start: 0.7356 (t) cc_final: 0.7020 (p) REVERT: G 32 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6034 (tt) REVERT: G 55 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.6117 (mpt90) REVERT: G 111 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5856 (mmp80) REVERT: I 12 LYS cc_start: 0.5709 (OUTLIER) cc_final: 0.4916 (tmmt) outliers start: 133 outliers final: 90 residues processed: 510 average time/residue: 1.0784 time to fit residues: 641.3034 Evaluate side-chains 511 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 404 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 596 ARG Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 654 ILE Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 929 GLU Chi-restraints excluded: chain B residue 974 THR Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 444 MET Chi-restraints excluded: chain C residue 448 PHE Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 152 ARG Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain I residue 12 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 3.9990 chunk 204 optimal weight: 0.0170 chunk 218 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 95 optimal weight: 9.9990 chunk 171 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 197 optimal weight: 0.8980 chunk 206 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 143 optimal weight: 0.6980 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 187 GLN B 226 ASN B 357 GLN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS B 876 ASN B 954 GLN B1019 ASN D 50 HIS ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS F 390 GLN ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 20503 Z= 0.198 Angle : 0.870 82.059 28049 Z= 0.362 Chirality : 0.051 1.515 3044 Planarity : 0.005 0.065 3537 Dihedral : 10.918 150.909 2889 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.20 % Allowed : 32.84 % Favored : 62.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.17), residues: 2455 helix: 0.40 (0.15), residues: 1227 sheet: -0.96 (0.42), residues: 155 loop : -1.13 (0.20), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP F 274 HIS 0.006 0.001 HIS C 246 PHE 0.027 0.001 PHE D 138 TYR 0.025 0.001 TYR F 108 ARG 0.012 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 423 time to evaluate : 2.199 Fit side-chains REVERT: A 65 ASP cc_start: 0.7605 (t70) cc_final: 0.7006 (t70) REVERT: B 90 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.6982 (mt0) REVERT: B 145 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7885 (mp10) REVERT: B 163 GLN cc_start: 0.6511 (OUTLIER) cc_final: 0.6188 (mt0) REVERT: B 176 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7651 (tm) REVERT: B 184 ARG cc_start: 0.6544 (ttm110) cc_final: 0.6261 (ttm110) REVERT: B 191 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8061 (m) REVERT: B 218 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6811 (mtp85) REVERT: B 593 GLU cc_start: 0.8308 (tp30) cc_final: 0.8032 (tp30) REVERT: B 596 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7952 (mtt90) REVERT: B 765 ARG cc_start: 0.7290 (mtm110) cc_final: 0.6735 (ptp-110) REVERT: B 838 LEU cc_start: 0.6913 (mt) cc_final: 0.6448 (mt) REVERT: C 55 PHE cc_start: 0.6985 (OUTLIER) cc_final: 0.6722 (t80) REVERT: C 183 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7912 (tm) REVERT: C 229 MET cc_start: 0.7475 (tpp) cc_final: 0.7207 (tpp) REVERT: C 323 PHE cc_start: 0.7003 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: C 448 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.7148 (p90) REVERT: C 460 LYS cc_start: 0.6755 (tptt) cc_final: 0.6102 (ttmm) REVERT: E 71 TYR cc_start: 0.6551 (m-10) cc_final: 0.6078 (m-10) REVERT: F 152 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.6118 (mtp85) REVERT: F 253 GLU cc_start: 0.6163 (tp30) cc_final: 0.5787 (tp30) REVERT: F 371 VAL cc_start: 0.7303 (t) cc_final: 0.6995 (p) REVERT: G 34 ARG cc_start: 0.5316 (mtt90) cc_final: 0.4723 (ptm160) REVERT: G 111 ARG cc_start: 0.6062 (OUTLIER) cc_final: 0.5820 (mmp80) REVERT: I 12 LYS cc_start: 0.5584 (OUTLIER) cc_final: 0.4802 (tmmt) REVERT: I 29 MET cc_start: 0.6738 (OUTLIER) cc_final: 0.6422 (mmm) outliers start: 86 outliers final: 46 residues processed: 478 average time/residue: 1.0955 time to fit residues: 606.9985 Evaluate side-chains 461 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 400 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 572 ILE Chi-restraints excluded: chain B residue 596 ARG Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 974 THR Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 448 PHE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 152 ARG Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain I residue 29 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 242 optimal weight: 7.9990 chunk 222 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 118 optimal weight: 0.0670 chunk 153 optimal weight: 6.9990 overall best weight: 1.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 187 GLN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS B 891 ASN B 954 GLN B1019 ASN C 463 GLN D 50 HIS ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS F 390 GLN ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 20503 Z= 0.230 Angle : 0.892 82.427 28049 Z= 0.370 Chirality : 0.051 1.510 3044 Planarity : 0.005 0.065 3537 Dihedral : 10.766 150.085 2882 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.76 % Allowed : 33.58 % Favored : 62.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.55 (0.17), residues: 2455 helix: 0.40 (0.15), residues: 1223 sheet: -0.99 (0.41), residues: 162 loop : -1.09 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP F 274 HIS 0.007 0.001 HIS C 246 PHE 0.027 0.001 PHE D 138 TYR 0.027 0.001 TYR F 108 ARG 0.012 0.000 ARG B 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4910 Ramachandran restraints generated. 2455 Oldfield, 0 Emsley, 2455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 413 time to evaluate : 2.313 Fit side-chains revert: symmetry clash REVERT: A 65 ASP cc_start: 0.7623 (t70) cc_final: 0.7018 (t70) REVERT: B 90 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.6951 (mt0) REVERT: B 145 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7900 (mp10) REVERT: B 163 GLN cc_start: 0.6466 (OUTLIER) cc_final: 0.6126 (mt0) REVERT: B 176 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7735 (tm) REVERT: B 184 ARG cc_start: 0.6566 (ttm110) cc_final: 0.6287 (ttm110) REVERT: B 191 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.8066 (m) REVERT: B 218 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6757 (mtp85) REVERT: B 593 GLU cc_start: 0.8283 (tp30) cc_final: 0.7974 (tp30) REVERT: B 596 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7964 (mtt90) REVERT: B 765 ARG cc_start: 0.7304 (mtm110) cc_final: 0.6747 (ptp-110) REVERT: B 838 LEU cc_start: 0.6978 (mt) cc_final: 0.6496 (mt) REVERT: C 55 PHE cc_start: 0.6997 (OUTLIER) cc_final: 0.6708 (t80) REVERT: C 183 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7936 (tm) REVERT: C 229 MET cc_start: 0.7481 (tpp) cc_final: 0.7257 (tpp) REVERT: C 316 MET cc_start: 0.8183 (mmm) cc_final: 0.7711 (mmp) REVERT: C 323 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.6648 (m-80) REVERT: C 448 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7207 (p90) REVERT: D 164 GLN cc_start: 0.6058 (pp30) cc_final: 0.5373 (pt0) REVERT: E 71 TYR cc_start: 0.6543 (m-10) cc_final: 0.6098 (m-10) REVERT: F 253 GLU cc_start: 0.6318 (tp30) cc_final: 0.5969 (tp30) REVERT: F 371 VAL cc_start: 0.7320 (t) cc_final: 0.7006 (p) REVERT: G 34 ARG cc_start: 0.5239 (mtt90) cc_final: 0.4718 (ptm160) REVERT: G 111 ARG cc_start: 0.6125 (OUTLIER) cc_final: 0.5797 (mmp80) REVERT: I 12 LYS cc_start: 0.5663 (OUTLIER) cc_final: 0.4861 (tmmt) REVERT: I 29 MET cc_start: 0.6712 (mtt) cc_final: 0.6413 (mmm) outliers start: 77 outliers final: 54 residues processed: 461 average time/residue: 1.1193 time to fit residues: 600.9865 Evaluate side-chains 468 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 401 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 596 ARG Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 819 SER Chi-restraints excluded: chain B residue 869 HIS Chi-restraints excluded: chain B residue 974 THR Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 185 PHE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 448 PHE Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 152 ARG Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain G residue 43 PHE Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain I residue 12 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 9.9990 chunk 59 optimal weight: 0.0050 chunk 177 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 53 optimal weight: 0.0470 chunk 193 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 198 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 169 optimal weight: 0.0070 overall best weight: 2.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN B 187 GLN B 226 ASN B 357 GLN ** B 623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS B 891 ASN B 954 GLN B1019 ASN ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS F 174 GLN F 390 GLN ** F 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.151446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127614 restraints weight = 28137.247| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.78 r_work: 0.3331 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 20503 Z= 0.255 Angle : 0.904 82.445 28049 Z= 0.376 Chirality : 0.052 1.512 3044 Planarity : 0.005 0.066 3537 Dihedral : 10.788 147.793 2882 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.20 % Allowed : 33.33 % Favored : 62.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.17), residues: 2455 helix: 0.33 (0.14), residues: 1229 sheet: -0.84 (0.42), residues: 155 loop : -1.13 (0.20), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP F 274 HIS 0.007 0.001 HIS C 246 PHE 0.030 0.001 PHE D 138 TYR 0.036 0.002 TYR F 108 ARG 0.011 0.000 ARG B 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9099.25 seconds wall clock time: 163 minutes 24.73 seconds (9804.73 seconds total)