Starting phenix.real_space_refine on Sat Apr 6 13:14:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvq_41648/04_2024/8tvq_41648_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvq_41648/04_2024/8tvq_41648.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvq_41648/04_2024/8tvq_41648_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvq_41648/04_2024/8tvq_41648_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvq_41648/04_2024/8tvq_41648_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvq_41648/04_2024/8tvq_41648.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvq_41648/04_2024/8tvq_41648.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvq_41648/04_2024/8tvq_41648_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvq_41648/04_2024/8tvq_41648_trim_updated.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.067 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: 8 Type Number sf(0) Gaussians Zn 8 6.06 5 P 101 5.49 5 Mg 1 5.21 5 S 160 5.16 5 C 19075 2.51 5 N 5454 2.21 5 O 6055 1.98 5 H 26856 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 85": "OD1" <-> "OD2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 481": "OD1" <-> "OD2" Residue "A PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 893": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 932": "OE1" <-> "OE2" Residue "A PHE 1225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1410": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 581": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 677": "OE1" <-> "OE2" Residue "B PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1041": "OE1" <-> "OE2" Residue "B TYR 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 67": "OD1" <-> "OD2" Residue "H TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 27": "OE1" <-> "OE2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 57710 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 20724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1356, 20724 Classifications: {'peptide': 1356} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1293} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 10, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 102 Chain: "B" Number of atoms: 16000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 16000 Classifications: {'peptide': 1041} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 45, 'TRANS': 995} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 4, 'PHE%COO:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 109 Chain: "C" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 4148 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "E" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3548 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1198 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 75} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2090 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 2 Chain: "I" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1138 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 141 Chain: "J" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1074 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1674 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "L" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 751 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "M" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 2171 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 433} Link IDs: {'CIS': 1, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 867 Unresolved non-hydrogen angles: 1300 Unresolved non-hydrogen dihedrals: 434 Planarities with less than four sites: {'UNK:plan-1': 433} Unresolved non-hydrogen planarities: 433 Chain: "N" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 1462 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "T" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 1427 Unusual residues: {'TTD': 1} Classifications: {'DNA': 44, 'undetermined': 1} Modifications used: {'3*END': 1} Link IDs: {'p': 1, 'rna3p': 42, None: 1} Not linked: pdbres=" DC T 17 " pdbres="TTD T 18 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "R" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 296 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1554 SG CYS A 110 90.394 70.141 124.291 1.00259.78 S ATOM 2450 SG CYS A 167 90.699 67.733 123.908 1.00252.81 S ATOM 1042 SG CYS A 77 45.458 77.186 104.824 1.00216.29 S ATOM 35812 SG CYS B1163 56.318 86.408 113.635 1.00226.00 S ATOM 35848 SG CYS B1166 58.980 83.392 112.756 1.00224.15 S ATOM 36138 SG CYS B1185 58.220 83.873 115.644 1.00235.98 S ATOM 38117 SG CYS C 92 11.783 78.328 45.049 1.00228.14 S ATOM 38161 SG CYS C 95 15.735 79.280 45.440 1.00227.36 S ATOM 48666 SG CYS I 103 112.732 49.088 34.345 1.00284.96 S ATOM 48705 SG CYS I 106 115.566 47.775 35.857 1.00306.21 S ATOM 48960 SG CYS J 7 43.598 73.741 32.481 1.00175.49 S ATOM 49557 SG CYS J 45 46.153 75.674 29.974 1.00169.58 S ATOM 51704 SG CYS L 31 29.867 38.339 57.855 1.00251.49 S ATOM 51739 SG CYS L 34 31.331 36.761 54.976 1.00269.29 S ATOM 51998 SG CYS L 51 32.363 36.129 57.471 1.00256.32 S Time building chain proxies: 19.56, per 1000 atoms: 0.34 Number of scatterers: 57710 At special positions: 0 Unit cell: (151.96, 155.44, 161.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 8 29.99 S 160 16.00 P 101 15.00 Mg 1 11.99 O 6055 8.00 N 5454 7.00 C 19075 6.00 H 26856 1.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 40.85 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7300 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 152 helices and 43 sheets defined 41.5% alpha, 13.5% beta 33 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 27.47 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 93 through 103 removed outlier: 5.066A pdb=" N ALA A 97 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS A 103 " --> pdb=" O LYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 131 through 144 removed outlier: 4.213A pdb=" N THR A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 261 through 281 removed outlier: 3.571A pdb=" N ASP A 268 " --> pdb=" O PHE A 264 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 277 " --> pdb=" O ASN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 304 removed outlier: 3.715A pdb=" N ALA A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 419 through 422 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 472 through 478 removed outlier: 3.528A pdb=" N SER A 476 " --> pdb=" O SER A 473 " (cutoff:3.500A) Proline residue: A 477 - end of helix Processing helix chain 'A' and resid 495 through 503 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 535 removed outlier: 3.770A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 removed outlier: 3.527A pdb=" N TYR A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.547A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 622 No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 629 through 636 Processing helix chain 'A' and resid 639 through 658 removed outlier: 4.361A pdb=" N LYS A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 673 through 698 Processing helix chain 'A' and resid 710 through 735 Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 795 through 797 No H-bonds generated for 'chain 'A' and resid 795 through 797' Processing helix chain 'A' and resid 804 through 806 No H-bonds generated for 'chain 'A' and resid 804 through 806' Processing helix chain 'A' and resid 810 through 845 removed outlier: 3.685A pdb=" N GLU A 822 " --> pdb=" O MET A 818 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLY A 835 " --> pdb=" O THR A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 890 through 897 removed outlier: 3.856A pdb=" N GLU A 894 " --> pdb=" O ASP A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 912 No H-bonds generated for 'chain 'A' and resid 910 through 912' Processing helix chain 'A' and resid 923 through 946 removed outlier: 3.714A pdb=" N GLU A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 971 Processing helix chain 'A' and resid 983 through 996 Processing helix chain 'A' and resid 1005 through 1014 Processing helix chain 'A' and resid 1016 through 1025 Processing helix chain 'A' and resid 1028 through 1033 Processing helix chain 'A' and resid 1039 through 1056 Processing helix chain 'A' and resid 1064 through 1077 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1099 through 1105 Processing helix chain 'A' and resid 1122 through 1124 No H-bonds generated for 'chain 'A' and resid 1122 through 1124' Processing helix chain 'A' and resid 1128 through 1137 Processing helix chain 'A' and resid 1143 through 1145 No H-bonds generated for 'chain 'A' and resid 1143 through 1145' Processing helix chain 'A' and resid 1199 through 1205 Processing helix chain 'A' and resid 1209 through 1219 Processing helix chain 'A' and resid 1258 through 1270 removed outlier: 4.332A pdb=" N LEU A1268 " --> pdb=" O GLU A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 4.050A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1326 No H-bonds generated for 'chain 'A' and resid 1324 through 1326' Processing helix chain 'A' and resid 1332 through 1338 Processing helix chain 'A' and resid 1341 through 1359 removed outlier: 3.941A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1376 Processing helix chain 'A' and resid 1396 through 1400 Processing helix chain 'A' and resid 1406 through 1415 Processing helix chain 'A' and resid 1424 through 1430 Processing helix chain 'A' and resid 1437 through 1439 No H-bonds generated for 'chain 'A' and resid 1437 through 1439' Processing helix chain 'B' and resid 28 through 41 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 308 through 323 Proline residue: B 316 - end of helix removed outlier: 3.526A pdb=" N PHE B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 338 Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 368 through 389 removed outlier: 4.554A pdb=" N LYS B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 379 " --> pdb=" O PHE B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 409 through 434 Processing helix chain 'B' and resid 443 through 463 removed outlier: 3.532A pdb=" N ASN B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 496 removed outlier: 3.631A pdb=" N SER B 493 " --> pdb=" O SER B 489 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 552 through 560 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 582 through 584 No H-bonds generated for 'chain 'B' and resid 582 through 584' Processing helix chain 'B' and resid 593 through 606 removed outlier: 4.067A pdb=" N ARG B 605 " --> pdb=" O ARG B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 670 Processing helix chain 'B' and resid 681 through 687 Processing helix chain 'B' and resid 695 through 700 removed outlier: 3.796A pdb=" N GLU B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N SER B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 695 through 700' Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 712 through 715 No H-bonds generated for 'chain 'B' and resid 712 through 715' Processing helix chain 'B' and resid 745 through 748 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 759 through 761 No H-bonds generated for 'chain 'B' and resid 759 through 761' Processing helix chain 'B' and resid 764 through 775 removed outlier: 3.953A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 812 removed outlier: 3.624A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1014 through 1020 Proline residue: B1018 - end of helix Processing helix chain 'B' and resid 1023 through 1038 removed outlier: 4.378A pdb=" N GLU B1028 " --> pdb=" O HIS B1025 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B1032 " --> pdb=" O CYS B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1062 Processing helix chain 'B' and resid 1099 through 1101 No H-bonds generated for 'chain 'B' and resid 1099 through 1101' Processing helix chain 'B' and resid 1132 through 1141 Processing helix chain 'B' and resid 1144 through 1153 removed outlier: 3.619A pdb=" N ARG B1150 " --> pdb=" O PHE B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 60 through 69 removed outlier: 3.693A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 240 through 266 Processing helix chain 'E' and resid 7 through 26 Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 118 through 125 Proline residue: E 125 - end of helix Processing helix chain 'E' and resid 137 through 141 Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 87 through 102 Processing helix chain 'F' and resid 117 through 127 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 117 through 121 Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 44 through 52 removed outlier: 4.340A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 62 removed outlier: 3.610A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 52 removed outlier: 4.103A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 116 Processing helix chain 'M' and resid 299 through 314 Processing helix chain 'M' and resid 329 through 339 removed outlier: 3.602A pdb=" N UNK M 333 " --> pdb=" O UNK M 329 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N UNK M 338 " --> pdb=" O UNK M 334 " (cutoff:3.500A) Processing helix chain 'M' and resid 355 through 368 removed outlier: 4.979A pdb=" N UNK M 360 " --> pdb=" O UNK M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 381 through 385 Processing helix chain 'M' and resid 395 through 401 Processing helix chain 'M' and resid 403 through 405 No H-bonds generated for 'chain 'M' and resid 403 through 405' Processing helix chain 'M' and resid 418 through 420 No H-bonds generated for 'chain 'M' and resid 418 through 420' Processing helix chain 'M' and resid 427 through 434 removed outlier: 3.717A pdb=" N UNK M 434 " --> pdb=" O UNK M 430 " (cutoff:3.500A) Processing helix chain 'M' and resid 452 through 462 removed outlier: 3.977A pdb=" N UNK M 457 " --> pdb=" O UNK M 453 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N UNK M 458 " --> pdb=" O UNK M 454 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N UNK M 460 " --> pdb=" O UNK M 456 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N UNK M 461 " --> pdb=" O UNK M 457 " (cutoff:3.500A) Processing helix chain 'M' and resid 470 through 476 removed outlier: 3.577A pdb=" N UNK M 475 " --> pdb=" O UNK M 471 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 483 Processing helix chain 'M' and resid 494 through 511 removed outlier: 4.202A pdb=" N UNK M 510 " --> pdb=" O UNK M 506 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N UNK M 511 " --> pdb=" O UNK M 507 " (cutoff:3.500A) Processing helix chain 'M' and resid 517 through 519 No H-bonds generated for 'chain 'M' and resid 517 through 519' Processing helix chain 'M' and resid 538 through 548 removed outlier: 3.593A pdb=" N UNK M 545 " --> pdb=" O UNK M 541 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N UNK M 546 " --> pdb=" O UNK M 542 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N UNK M 547 " --> pdb=" O UNK M 543 " (cutoff:3.500A) Processing helix chain 'M' and resid 553 through 555 No H-bonds generated for 'chain 'M' and resid 553 through 555' Processing helix chain 'M' and resid 561 through 574 removed outlier: 4.311A pdb=" N UNK M 574 " --> pdb=" O UNK M 570 " (cutoff:3.500A) Processing helix chain 'M' and resid 647 through 649 No H-bonds generated for 'chain 'M' and resid 647 through 649' Processing helix chain 'M' and resid 651 through 665 Processing helix chain 'M' and resid 677 through 688 Processing helix chain 'M' and resid 692 through 697 Processing helix chain 'M' and resid 708 through 719 Processing helix chain 'M' and resid 730 through 735 removed outlier: 3.508A pdb=" N UNK M 734 " --> pdb=" O UNK M 730 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N UNK M 735 " --> pdb=" O UNK M 731 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 730 through 735' Processing helix chain 'M' and resid 754 through 764 removed outlier: 4.289A pdb=" N UNK M 759 " --> pdb=" O UNK M 755 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N UNK M 760 " --> pdb=" O UNK M 756 " (cutoff:3.500A) Processing helix chain 'M' and resid 784 through 796 Processing sheet with id= A, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= B, first strand: chain 'A' and resid 151 through 153 Processing sheet with id= C, first strand: chain 'A' and resid 173 through 177 Processing sheet with id= D, first strand: chain 'A' and resid 348 through 352 Processing sheet with id= E, first strand: chain 'A' and resid 353 through 355 removed outlier: 5.683A pdb=" N PHE A 468 " --> pdb=" O SER A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 363 through 367 removed outlier: 6.168A pdb=" N ARG A 459 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A 366 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS A 461 " --> pdb=" O VAL A 366 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 375 through 379 Processing sheet with id= H, first strand: chain 'A' and resid 404 through 406 Processing sheet with id= I, first strand: chain 'A' and resid 849 through 851 removed outlier: 3.798A pdb=" N MET A 849 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 857 " --> pdb=" O MET A 849 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 855 " --> pdb=" O HIS A 851 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 878 through 882 Processing sheet with id= K, first strand: chain 'A' and resid 1115 through 1118 removed outlier: 3.502A pdb=" N THR A1308 " --> pdb=" O LEU A1116 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1290 through 1292 Processing sheet with id= M, first strand: chain 'A' and resid 606 through 608 removed outlier: 6.375A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 1147 through 1150 removed outlier: 6.763A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 68 through 71 Processing sheet with id= P, first strand: chain 'B' and resid 95 through 97 removed outlier: 5.448A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= R, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= S, first strand: chain 'B' and resid 215 through 218 removed outlier: 3.608A pdb=" N GLN B 215 " --> pdb=" O ASP B 407 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 224 through 227 removed outlier: 3.725A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 543 through 545 Processing sheet with id= V, first strand: chain 'B' and resid 588 through 590 removed outlier: 3.707A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 626 " --> pdb=" O PHE B 581 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 1086 through 1092 removed outlier: 4.066A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B1010 " --> pdb=" O ALA B 826 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 853 through 862 removed outlier: 3.652A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 964 " --> pdb=" O ASP B 861 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 979 through 981 Processing sheet with id= Z, first strand: chain 'B' and resid 1159 through 1163 Processing sheet with id= AA, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id= AB, first strand: chain 'B' and resid 839 through 842 removed outlier: 7.480A pdb=" N MET B 841 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR B 993 " --> pdb=" O MET B 841 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.681A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 96 through 104 removed outlier: 5.846A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 111 through 114 Processing sheet with id= AF, first strand: chain 'E' and resid 60 through 62 Processing sheet with id= AG, first strand: chain 'E' and resid 107 through 112 removed outlier: 6.986A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N TYR E 112 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N PHE E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'E' and resid 152 through 155 Processing sheet with id= AI, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AJ, first strand: chain 'H' and resid 7 through 11 removed outlier: 6.068A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS H 37 " --> pdb=" O GLU H 126 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'I' and resid 16 through 19 Processing sheet with id= AL, first strand: chain 'I' and resid 83 through 87 Processing sheet with id= AM, first strand: chain 'K' and resid 19 through 23 Processing sheet with id= AN, first strand: chain 'L' and resid 29 through 31 Processing sheet with id= AO, first strand: chain 'M' and resid 318 through 320 removed outlier: 3.533A pdb=" N UNK M 318 " --> pdb=" O UNK M 440 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N UNK M 442 " --> pdb=" O UNK M 318 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N UNK M 413 " --> pdb=" O UNK M 441 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N UNK M 443 " --> pdb=" O UNK M 413 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N UNK M 415 " --> pdb=" O UNK M 443 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'M' and resid 349 through 352 Processing sheet with id= AQ, first strand: chain 'M' and resid 529 through 535 removed outlier: 5.400A pdb=" N UNK M 775 " --> pdb=" O UNK M 530 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N UNK M 532 " --> pdb=" O UNK M 775 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N UNK M 777 " --> pdb=" O UNK M 532 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N UNK M 534 " --> pdb=" O UNK M 777 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N UNK M 779 " --> pdb=" O UNK M 534 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N UNK M 749 " --> pdb=" O UNK M 778 " (cutoff:3.500A) removed outlier: 12.226A pdb=" N UNK M 780 " --> pdb=" O UNK M 749 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N UNK M 726 " --> pdb=" O UNK M 672 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N UNK M 674 " --> pdb=" O UNK M 726 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N UNK M 728 " --> pdb=" O UNK M 674 " (cutoff:3.500A) 1047 hydrogen bonds defined for protein. 2889 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 24.19 Time building geometry restraints manager: 42.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 26810 1.03 - 1.23: 530 1.23 - 1.43: 12605 1.43 - 1.63: 18205 1.63 - 1.82: 266 Bond restraints: 58416 Sorted by residual: bond pdb=" O3' TTD T 18 " pdb=" P DT T 19 " ideal model delta sigma weight residual 1.600 1.480 0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" O3' G R 6 " pdb=" P A R 7 " ideal model delta sigma weight residual 1.607 1.553 0.054 1.50e-02 4.44e+03 1.28e+01 bond pdb=" O3' A R 5 " pdb=" P G R 6 " ideal model delta sigma weight residual 1.607 1.565 0.042 1.50e-02 4.44e+03 7.75e+00 bond pdb=" O3' G R 4 " pdb=" P A R 5 " ideal model delta sigma weight residual 1.607 1.643 -0.036 1.50e-02 4.44e+03 5.66e+00 bond pdb=" O3R TTD T 18 " pdb=" PB TTD T 18 " ideal model delta sigma weight residual 1.647 1.694 -0.047 2.00e-02 2.50e+03 5.48e+00 ... (remaining 58411 not shown) Histogram of bond angle deviations from ideal: 87.48 - 96.81: 7 96.81 - 106.14: 1420 106.14 - 115.47: 72084 115.47 - 124.79: 28453 124.79 - 134.12: 2530 Bond angle restraints: 104494 Sorted by residual: angle pdb=" N PRO B 877 " pdb=" CA PRO B 877 " pdb=" CB PRO B 877 " ideal model delta sigma weight residual 103.35 111.10 -7.75 8.70e-01 1.32e+00 7.94e+01 angle pdb=" N PRO A 321 " pdb=" CA PRO A 321 " pdb=" CB PRO A 321 " ideal model delta sigma weight residual 103.31 111.11 -7.80 8.90e-01 1.26e+00 7.67e+01 angle pdb=" O3' DC T 17 " pdb=" C3' DC T 17 " pdb=" H3' DC T 17 " ideal model delta sigma weight residual 109.00 96.84 12.16 1.50e+00 4.44e-01 6.57e+01 angle pdb=" N PRO A 312 " pdb=" CA PRO A 312 " pdb=" CB PRO A 312 " ideal model delta sigma weight residual 103.25 111.12 -7.87 1.05e+00 9.07e-01 5.61e+01 angle pdb=" N PRO F 106 " pdb=" CA PRO F 106 " pdb=" CB PRO F 106 " ideal model delta sigma weight residual 103.25 111.10 -7.85 1.05e+00 9.07e-01 5.59e+01 ... (remaining 104489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 26407 35.87 - 71.73: 935 71.73 - 107.60: 21 107.60 - 143.46: 2 143.46 - 179.33: 5 Dihedral angle restraints: 27370 sinusoidal: 14723 harmonic: 12647 Sorted by residual: dihedral pdb=" CA GLU F 127 " pdb=" C GLU F 127 " pdb=" N LYS F 128 " pdb=" CA LYS F 128 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA ARG H 87 " pdb=" C ARG H 87 " pdb=" N SER H 88 " pdb=" CA SER H 88 " ideal model delta harmonic sigma weight residual -180.00 -157.40 -22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" C4' TTD T 18 " pdb=" C5R TTD T 18 " pdb=" O5R TTD T 18 " pdb=" PB TTD T 18 " ideal model delta sinusoidal sigma weight residual 241.46 92.03 149.43 1 3.00e+01 1.11e-03 1.99e+01 ... (remaining 27367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4612 0.083 - 0.165: 361 0.165 - 0.248: 16 0.248 - 0.331: 1 0.331 - 0.414: 1 Chirality restraints: 4991 Sorted by residual: chirality pdb=" C3' DC T 17 " pdb=" C4' DC T 17 " pdb=" O3' DC T 17 " pdb=" C2' DC T 17 " both_signs ideal model delta sigma weight residual False -2.66 -2.25 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" C3' DA N 15 " pdb=" C4' DA N 15 " pdb=" O3' DA N 15 " pdb=" C2' DA N 15 " both_signs ideal model delta sigma weight residual False -2.66 -2.35 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C5 TTD T 18 " pdb=" C4 TTD T 18 " pdb=" C6 TTD T 18 " pdb=" C5T TTD T 18 " both_signs ideal model delta sigma weight residual False -2.76 -2.52 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 4988 not shown) Planarity restraints: 8420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC T 16 " 0.003 2.00e-02 2.50e+03 2.16e-02 1.28e+01 pdb=" N1 DC T 16 " 0.039 2.00e-02 2.50e+03 pdb=" C2 DC T 16 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DC T 16 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DC T 16 " -0.022 2.00e-02 2.50e+03 pdb=" C4 DC T 16 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC T 16 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DC T 16 " 0.011 2.00e-02 2.50e+03 pdb=" C6 DC T 16 " -0.005 2.00e-02 2.50e+03 pdb=" H5 DC T 16 " 0.026 2.00e-02 2.50e+03 pdb=" H6 DC T 16 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 247 " 0.049 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO A 248 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 248 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 248 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' TTD T 18 " 0.013 2.00e-02 2.50e+03 1.51e-02 5.14e+00 pdb=" N1 TTD T 18 " -0.011 2.00e-02 2.50e+03 pdb=" C2 TTD T 18 " 0.000 2.00e-02 2.50e+03 pdb=" O2 TTD T 18 " 0.001 2.00e-02 2.50e+03 pdb=" N3 TTD T 18 " 0.004 2.00e-02 2.50e+03 pdb=" C4 TTD T 18 " -0.019 2.00e-02 2.50e+03 pdb=" O4 TTD T 18 " 0.005 2.00e-02 2.50e+03 pdb=" C5 TTD T 18 " 0.029 2.00e-02 2.50e+03 pdb=" C6 TTD T 18 " -0.023 2.00e-02 2.50e+03 ... (remaining 8417 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.78: 452 1.78 - 2.49: 43030 2.49 - 3.19: 179636 3.19 - 3.90: 234996 3.90 - 4.60: 366109 Nonbonded interactions: 824223 Sorted by model distance: nonbonded pdb="HE22 GLN B 481 " pdb="HO2' G R 6 " model vdw 1.078 2.100 nonbonded pdb=" OE2 GLU A1404 " pdb=" OP1 DC T 17 " model vdw 1.187 2.800 nonbonded pdb="HH12 ARG A1386 " pdb=" H1' DC T 16 " model vdw 1.243 2.270 nonbonded pdb="HE22 GLN B 481 " pdb=" O2' G R 6 " model vdw 1.363 1.850 nonbonded pdb=" H22 DG N 34 " pdb=" O2 DC T 14 " model vdw 1.373 1.850 ... (remaining 824218 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 group one per residue 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.680 Extract box with map and model: 12.970 Check model and map are aligned: 0.680 Set scattering table: 0.420 Process input model: 184.590 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 205.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 31560 Z= 0.255 Angle : 0.740 9.705 43205 Z= 0.429 Chirality : 0.044 0.414 4991 Planarity : 0.005 0.073 5289 Dihedral : 15.381 149.426 11660 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.35 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: -1.44 (0.14), residues: 3368 helix: -1.09 (0.14), residues: 1108 sheet: -1.12 (0.23), residues: 492 loop : -0.69 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 552 HIS 0.007 0.001 HIS B 761 PHE 0.018 0.002 PHE J 60 TYR 0.016 0.002 TYR B 811 ARG 0.018 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 582 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 582 time to evaluate : 3.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9560 (tp40) cc_final: 0.9107 (tm-30) REVERT: A 95 PHE cc_start: 0.9532 (m-10) cc_final: 0.9215 (m-10) REVERT: A 466 SER cc_start: 0.9347 (p) cc_final: 0.9112 (p) REVERT: A 504 LEU cc_start: 0.9417 (mt) cc_final: 0.9109 (mt) REVERT: A 511 ILE cc_start: 0.9555 (tp) cc_final: 0.8612 (tp) REVERT: A 535 THR cc_start: 0.9040 (t) cc_final: 0.8832 (p) REVERT: A 550 LEU cc_start: 0.9405 (mt) cc_final: 0.9198 (mt) REVERT: A 613 ILE cc_start: 0.9344 (mp) cc_final: 0.8949 (mp) REVERT: A 662 PHE cc_start: 0.8820 (t80) cc_final: 0.8605 (t80) REVERT: A 663 SER cc_start: 0.9293 (p) cc_final: 0.9089 (p) REVERT: A 791 ASP cc_start: 0.8460 (t0) cc_final: 0.8127 (t0) REVERT: A 841 LEU cc_start: 0.9371 (tp) cc_final: 0.9150 (tp) REVERT: A 846 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8603 (tm-30) REVERT: A 1116 LEU cc_start: 0.9398 (mt) cc_final: 0.9095 (mt) REVERT: A 1285 MET cc_start: 0.8576 (mmp) cc_final: 0.8077 (mmm) REVERT: A 1433 MET cc_start: 0.8711 (ttt) cc_final: 0.8474 (ttt) REVERT: B 360 PHE cc_start: 0.9538 (t80) cc_final: 0.9093 (t80) REVERT: B 407 ASP cc_start: 0.9059 (m-30) cc_final: 0.8836 (m-30) REVERT: B 696 GLU cc_start: 0.9478 (mm-30) cc_final: 0.9236 (mm-30) REVERT: B 782 LEU cc_start: 0.9168 (mt) cc_final: 0.8815 (mt) REVERT: B 834 ASN cc_start: 0.9235 (p0) cc_final: 0.8776 (p0) REVERT: B 843 GLN cc_start: 0.9555 (tp40) cc_final: 0.9176 (tp40) REVERT: B 980 PHE cc_start: 0.8292 (m-10) cc_final: 0.7584 (m-10) REVERT: B 1098 MET cc_start: 0.8983 (mmp) cc_final: 0.8410 (mmm) REVERT: B 1149 GLU cc_start: 0.9462 (tm-30) cc_final: 0.9019 (tm-30) REVERT: B 1158 PHE cc_start: 0.8624 (t80) cc_final: 0.8095 (t80) REVERT: B 1169 MET cc_start: 0.8843 (mmp) cc_final: 0.8629 (mmp) REVERT: C 61 GLU cc_start: 0.9006 (mp0) cc_final: 0.8637 (mp0) REVERT: E 1 MET cc_start: 0.8571 (mmm) cc_final: 0.8312 (mmm) REVERT: F 127 GLU cc_start: 0.8984 (pm20) cc_final: 0.8753 (pm20) REVERT: H 46 LEU cc_start: 0.9069 (mt) cc_final: 0.8765 (mt) REVERT: I 101 PHE cc_start: 0.8986 (m-80) cc_final: 0.8738 (m-80) REVERT: I 111 THR cc_start: 0.8961 (p) cc_final: 0.8559 (t) REVERT: J 32 GLU cc_start: 0.9413 (mm-30) cc_final: 0.9121 (mm-30) REVERT: J 36 LEU cc_start: 0.9676 (mt) cc_final: 0.9357 (mt) REVERT: K 76 GLN cc_start: 0.8980 (tt0) cc_final: 0.8545 (tt0) REVERT: K 106 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9194 (tm-30) REVERT: K 120 PHE cc_start: 0.6173 (m-80) cc_final: 0.5972 (m-10) outliers start: 0 outliers final: 0 residues processed: 582 average time/residue: 0.7626 time to fit residues: 718.1837 Evaluate side-chains 486 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 486 time to evaluate : 3.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 328 optimal weight: 3.9990 chunk 294 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 304 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 353 optimal weight: 50.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 GLN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN K 89 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 31560 Z= 0.374 Angle : 0.659 7.736 43205 Z= 0.367 Chirality : 0.041 0.191 4991 Planarity : 0.005 0.055 5289 Dihedral : 16.348 151.267 5254 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 24.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.64 % Favored : 91.30 % Rotamer: Outliers : 0.04 % Allowed : 1.80 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: -2.01 (0.14), residues: 3368 helix: -1.34 (0.13), residues: 1171 sheet: -1.64 (0.22), residues: 523 loop : -1.08 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 656 HIS 0.011 0.002 HIS A 80 PHE 0.028 0.002 PHE H 6 TYR 0.017 0.002 TYR B 303 ARG 0.009 0.001 ARG B 605 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 555 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 554 time to evaluate : 3.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9592 (tp40) cc_final: 0.9134 (tm-30) REVERT: A 95 PHE cc_start: 0.9457 (m-10) cc_final: 0.9197 (m-10) REVERT: A 234 MET cc_start: 0.9682 (mtp) cc_final: 0.9355 (mtp) REVERT: A 326 ARG cc_start: 0.9649 (tmm-80) cc_final: 0.9209 (tmm-80) REVERT: A 466 SER cc_start: 0.9376 (p) cc_final: 0.9125 (p) REVERT: A 504 LEU cc_start: 0.9421 (mt) cc_final: 0.9114 (mt) REVERT: A 676 MET cc_start: 0.9624 (mmt) cc_final: 0.9302 (mmm) REVERT: A 764 CYS cc_start: 0.7830 (p) cc_final: 0.7551 (p) REVERT: A 784 LEU cc_start: 0.9319 (mt) cc_final: 0.9018 (mt) REVERT: A 846 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8732 (tm-30) REVERT: A 878 ILE cc_start: 0.9088 (mm) cc_final: 0.8824 (mm) REVERT: A 1285 MET cc_start: 0.8498 (mmp) cc_final: 0.8040 (mmm) REVERT: A 1417 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7412 (tm-30) REVERT: B 407 ASP cc_start: 0.9175 (m-30) cc_final: 0.8880 (m-30) REVERT: B 484 ASN cc_start: 0.9042 (t0) cc_final: 0.8776 (t0) REVERT: B 782 LEU cc_start: 0.9267 (mt) cc_final: 0.8960 (mt) REVERT: B 834 ASN cc_start: 0.9342 (p0) cc_final: 0.8870 (p0) REVERT: B 946 ASN cc_start: 0.8317 (t0) cc_final: 0.7858 (p0) REVERT: B 969 ARG cc_start: 0.8073 (ptt180) cc_final: 0.7459 (ptt180) REVERT: B 980 PHE cc_start: 0.8354 (m-10) cc_final: 0.7635 (m-10) REVERT: B 1098 MET cc_start: 0.8971 (mmp) cc_final: 0.8319 (mmm) REVERT: B 1133 MET cc_start: 0.9274 (mmm) cc_final: 0.9063 (mmm) REVERT: B 1149 GLU cc_start: 0.9301 (tm-30) cc_final: 0.8678 (tm-30) REVERT: B 1158 PHE cc_start: 0.8613 (t80) cc_final: 0.8159 (t80) REVERT: B 1168 LEU cc_start: 0.9651 (mt) cc_final: 0.9419 (mt) REVERT: B 1169 MET cc_start: 0.8799 (mmp) cc_final: 0.8374 (mmp) REVERT: C 61 GLU cc_start: 0.8993 (mp0) cc_final: 0.8507 (mp0) REVERT: F 148 VAL cc_start: 0.9520 (p) cc_final: 0.9246 (p) REVERT: H 1 MET cc_start: 0.3812 (mmm) cc_final: 0.3034 (tpt) REVERT: H 46 LEU cc_start: 0.9059 (mt) cc_final: 0.8779 (mt) REVERT: I 101 PHE cc_start: 0.9011 (m-80) cc_final: 0.8799 (m-80) REVERT: I 111 THR cc_start: 0.8972 (p) cc_final: 0.8567 (t) REVERT: J 32 GLU cc_start: 0.9420 (mm-30) cc_final: 0.9120 (mm-30) REVERT: J 36 LEU cc_start: 0.9730 (mt) cc_final: 0.9446 (mt) REVERT: K 76 GLN cc_start: 0.8996 (tt0) cc_final: 0.8439 (tp40) outliers start: 1 outliers final: 1 residues processed: 555 average time/residue: 0.7257 time to fit residues: 647.2592 Evaluate side-chains 466 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 465 time to evaluate : 3.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 196 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 353 optimal weight: 50.0000 chunk 382 optimal weight: 8.9990 chunk 315 optimal weight: 7.9990 chunk 350 optimal weight: 40.0000 chunk 120 optimal weight: 2.9990 chunk 283 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 ASN ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31560 Z= 0.226 Angle : 0.547 6.078 43205 Z= 0.303 Chirality : 0.039 0.154 4991 Planarity : 0.004 0.050 5289 Dihedral : 16.213 144.206 5254 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.89 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: -1.47 (0.14), residues: 3368 helix: -0.68 (0.14), residues: 1159 sheet: -1.52 (0.22), residues: 504 loop : -0.89 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 656 HIS 0.006 0.001 HIS A 80 PHE 0.018 0.002 PHE A 482 TYR 0.019 0.002 TYR B1092 ARG 0.012 0.000 ARG B 605 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 571 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 571 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9573 (tp40) cc_final: 0.9273 (tm-30) REVERT: A 326 ARG cc_start: 0.9594 (tmm-80) cc_final: 0.8991 (tmm-80) REVERT: A 466 SER cc_start: 0.9349 (p) cc_final: 0.9126 (p) REVERT: A 504 LEU cc_start: 0.9434 (mt) cc_final: 0.9149 (mt) REVERT: A 676 MET cc_start: 0.9610 (mmt) cc_final: 0.9256 (mmm) REVERT: A 764 CYS cc_start: 0.7731 (p) cc_final: 0.7429 (p) REVERT: A 784 LEU cc_start: 0.9291 (mt) cc_final: 0.8987 (mt) REVERT: A 846 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8763 (tm-30) REVERT: A 878 ILE cc_start: 0.9045 (mm) cc_final: 0.8821 (mm) REVERT: A 1143 LEU cc_start: 0.9558 (tp) cc_final: 0.9312 (tt) REVERT: A 1285 MET cc_start: 0.8451 (mmp) cc_final: 0.7968 (mmm) REVERT: A 1405 THR cc_start: 0.9103 (p) cc_final: 0.8817 (m) REVERT: A 1417 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7314 (tm-30) REVERT: B 312 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8545 (tm-30) REVERT: B 452 THR cc_start: 0.8948 (m) cc_final: 0.8730 (p) REVERT: B 782 LEU cc_start: 0.9302 (mt) cc_final: 0.8901 (mt) REVERT: B 834 ASN cc_start: 0.9303 (p0) cc_final: 0.8784 (p0) REVERT: B 860 MET cc_start: 0.8899 (ppp) cc_final: 0.8620 (ppp) REVERT: B 946 ASN cc_start: 0.8341 (t0) cc_final: 0.7911 (p0) REVERT: B 980 PHE cc_start: 0.8427 (m-10) cc_final: 0.8104 (m-10) REVERT: B 1098 MET cc_start: 0.9046 (mmp) cc_final: 0.8310 (mmm) REVERT: B 1149 GLU cc_start: 0.9310 (tm-30) cc_final: 0.8616 (tm-30) REVERT: B 1158 PHE cc_start: 0.8543 (t80) cc_final: 0.8123 (t80) REVERT: C 61 GLU cc_start: 0.8984 (mp0) cc_final: 0.8604 (mp0) REVERT: I 111 THR cc_start: 0.8940 (p) cc_final: 0.8550 (t) REVERT: J 32 GLU cc_start: 0.9414 (mm-30) cc_final: 0.9128 (mm-30) REVERT: J 36 LEU cc_start: 0.9703 (mt) cc_final: 0.9471 (mt) REVERT: K 76 GLN cc_start: 0.8831 (tt0) cc_final: 0.8314 (tt0) REVERT: K 120 PHE cc_start: 0.6560 (m-80) cc_final: 0.6264 (m-10) outliers start: 0 outliers final: 0 residues processed: 571 average time/residue: 0.7170 time to fit residues: 658.6029 Evaluate side-chains 489 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 489 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 349 optimal weight: 70.0000 chunk 266 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 168 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 chunk 355 optimal weight: 30.0000 chunk 376 optimal weight: 50.0000 chunk 185 optimal weight: 4.9990 chunk 336 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN A 736 ASN ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1124 HIS B 110 HIS ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN B 975 GLN ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 31560 Z= 0.431 Angle : 0.697 8.043 43205 Z= 0.394 Chirality : 0.041 0.170 4991 Planarity : 0.006 0.060 5289 Dihedral : 16.336 148.217 5254 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 32.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.81 % Favored : 89.13 % Rotamer: Outliers : 0.04 % Allowed : 2.83 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: -2.45 (0.13), residues: 3368 helix: -1.50 (0.13), residues: 1163 sheet: -1.77 (0.22), residues: 513 loop : -1.58 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 656 HIS 0.009 0.002 HIS B 587 PHE 0.056 0.003 PHE B 638 TYR 0.021 0.003 TYR B 303 ARG 0.010 0.001 ARG B 605 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 536 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 535 time to evaluate : 3.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9586 (tp40) cc_final: 0.9343 (tm-30) REVERT: A 211 PHE cc_start: 0.9571 (m-10) cc_final: 0.9124 (m-10) REVERT: A 234 MET cc_start: 0.9705 (mtp) cc_final: 0.9230 (mtp) REVERT: A 326 ARG cc_start: 0.9649 (tmm-80) cc_final: 0.8983 (tmm-80) REVERT: A 504 LEU cc_start: 0.9442 (mt) cc_final: 0.9193 (mt) REVERT: A 619 LYS cc_start: 0.9309 (tttt) cc_final: 0.9087 (ttmm) REVERT: A 676 MET cc_start: 0.9641 (mmt) cc_final: 0.9277 (mmm) REVERT: A 764 CYS cc_start: 0.7981 (p) cc_final: 0.7732 (p) REVERT: A 784 LEU cc_start: 0.9334 (mt) cc_final: 0.9062 (mt) REVERT: A 846 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8744 (tm-30) REVERT: A 878 ILE cc_start: 0.9217 (mm) cc_final: 0.8904 (mm) REVERT: A 1048 ASN cc_start: 0.9483 (t0) cc_final: 0.9003 (t0) REVERT: A 1285 MET cc_start: 0.8631 (mmp) cc_final: 0.8159 (mmm) REVERT: A 1334 ASP cc_start: 0.9545 (m-30) cc_final: 0.9324 (m-30) REVERT: A 1372 VAL cc_start: 0.9491 (m) cc_final: 0.9177 (m) REVERT: A 1375 MET cc_start: 0.9374 (mtp) cc_final: 0.9169 (mtp) REVERT: A 1405 THR cc_start: 0.9412 (p) cc_final: 0.9136 (m) REVERT: B 174 LEU cc_start: 0.9441 (mp) cc_final: 0.9236 (mp) REVERT: B 310 MET cc_start: 0.9298 (tmm) cc_final: 0.9048 (tmm) REVERT: B 407 ASP cc_start: 0.9077 (m-30) cc_final: 0.8825 (m-30) REVERT: B 452 THR cc_start: 0.9030 (m) cc_final: 0.8821 (p) REVERT: B 484 ASN cc_start: 0.9153 (t0) cc_final: 0.8852 (t0) REVERT: B 834 ASN cc_start: 0.9324 (p0) cc_final: 0.8901 (p0) REVERT: B 860 MET cc_start: 0.8896 (ppp) cc_final: 0.8534 (ppp) REVERT: B 946 ASN cc_start: 0.8345 (t0) cc_final: 0.7790 (p0) REVERT: B 980 PHE cc_start: 0.8432 (m-10) cc_final: 0.7747 (m-10) REVERT: B 1098 MET cc_start: 0.9022 (mmp) cc_final: 0.8501 (mmm) REVERT: B 1138 MET cc_start: 0.8773 (mtp) cc_final: 0.8557 (mmp) REVERT: B 1149 GLU cc_start: 0.9327 (tm-30) cc_final: 0.8736 (tm-30) REVERT: B 1158 PHE cc_start: 0.8715 (t80) cc_final: 0.8318 (t80) REVERT: C 61 GLU cc_start: 0.9022 (mp0) cc_final: 0.8679 (mp0) REVERT: H 97 MET cc_start: 0.8852 (mmp) cc_final: 0.8561 (mmp) REVERT: H 121 LEU cc_start: 0.9567 (mm) cc_final: 0.9346 (mm) REVERT: I 101 PHE cc_start: 0.8912 (m-80) cc_final: 0.8711 (m-80) REVERT: I 111 THR cc_start: 0.9028 (p) cc_final: 0.8618 (t) REVERT: K 38 GLU cc_start: 0.8186 (tp30) cc_final: 0.7909 (tp30) REVERT: K 120 PHE cc_start: 0.6584 (m-80) cc_final: 0.6302 (m-10) REVERT: L 46 VAL cc_start: 0.7424 (m) cc_final: 0.6927 (t) REVERT: L 56 LEU cc_start: 0.9556 (mt) cc_final: 0.9222 (mp) outliers start: 1 outliers final: 0 residues processed: 536 average time/residue: 0.7386 time to fit residues: 634.3590 Evaluate side-chains 454 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 454 time to evaluate : 3.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 313 optimal weight: 0.5980 chunk 213 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 279 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 320 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 192 optimal weight: 0.8980 chunk 337 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 996 ASN A1124 HIS ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31560 Z= 0.214 Angle : 0.540 5.946 43205 Z= 0.299 Chirality : 0.039 0.157 4991 Planarity : 0.004 0.046 5289 Dihedral : 16.198 143.249 5254 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.36 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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 (0.14), residues: 3368 helix: -0.73 (0.14), residues: 1160 sheet: -1.63 (0.22), residues: 495 loop : -1.19 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 656 HIS 0.009 0.001 HIS C 167 PHE 0.019 0.002 PHE B 638 TYR 0.018 0.002 TYR B1092 ARG 0.027 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 561 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 561 time to evaluate : 3.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9573 (tp40) cc_final: 0.9318 (tm-30) REVERT: A 74 MET cc_start: 0.6772 (mtt) cc_final: 0.6244 (mmt) REVERT: A 281 HIS cc_start: 0.9335 (t-90) cc_final: 0.8961 (t-90) REVERT: A 326 ARG cc_start: 0.9625 (tmm-80) cc_final: 0.8947 (tmm-80) REVERT: A 504 LEU cc_start: 0.9433 (mt) cc_final: 0.8984 (mt) REVERT: A 619 LYS cc_start: 0.9298 (tttt) cc_final: 0.9049 (ttmm) REVERT: A 676 MET cc_start: 0.9592 (mmt) cc_final: 0.9231 (mmm) REVERT: A 764 CYS cc_start: 0.7925 (p) cc_final: 0.7646 (p) REVERT: A 784 LEU cc_start: 0.9315 (mt) cc_final: 0.9103 (mt) REVERT: A 841 LEU cc_start: 0.9372 (tp) cc_final: 0.9082 (tp) REVERT: A 846 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8703 (tm-30) REVERT: A 1048 ASN cc_start: 0.9434 (t0) cc_final: 0.8998 (t0) REVERT: A 1285 MET cc_start: 0.8549 (mmp) cc_final: 0.8063 (mmm) REVERT: A 1334 ASP cc_start: 0.9498 (m-30) cc_final: 0.9180 (m-30) REVERT: A 1372 VAL cc_start: 0.9409 (m) cc_final: 0.9134 (m) REVERT: A 1375 MET cc_start: 0.9353 (mtp) cc_final: 0.9135 (mtp) REVERT: B 310 MET cc_start: 0.9144 (tmm) cc_final: 0.8875 (tmm) REVERT: B 452 THR cc_start: 0.8947 (m) cc_final: 0.8740 (p) REVERT: B 782 LEU cc_start: 0.9280 (mt) cc_final: 0.8814 (mt) REVERT: B 834 ASN cc_start: 0.9359 (p0) cc_final: 0.8896 (p0) REVERT: B 860 MET cc_start: 0.8942 (ppp) cc_final: 0.8621 (ppp) REVERT: B 946 ASN cc_start: 0.8335 (t0) cc_final: 0.7766 (p0) REVERT: B 980 PHE cc_start: 0.8325 (m-10) cc_final: 0.8018 (m-10) REVERT: B 1098 MET cc_start: 0.9045 (mmp) cc_final: 0.8458 (mmm) REVERT: B 1149 GLU cc_start: 0.9316 (tm-30) cc_final: 0.8668 (tm-30) REVERT: B 1158 PHE cc_start: 0.8657 (t80) cc_final: 0.8060 (t80) REVERT: C 61 GLU cc_start: 0.9008 (mp0) cc_final: 0.8625 (mp0) REVERT: C 265 MET cc_start: 0.8421 (ttm) cc_final: 0.8182 (ttt) REVERT: E 1 MET cc_start: 0.9030 (mmm) cc_final: 0.8770 (mmm) REVERT: H 40 LEU cc_start: 0.9139 (tp) cc_final: 0.7844 (tp) REVERT: H 46 LEU cc_start: 0.9028 (mt) cc_final: 0.8819 (mt) REVERT: H 122 LEU cc_start: 0.9195 (mt) cc_final: 0.8790 (mt) REVERT: I 111 THR cc_start: 0.8961 (p) cc_final: 0.8579 (t) REVERT: J 32 GLU cc_start: 0.9412 (mm-30) cc_final: 0.9152 (mm-30) REVERT: J 36 LEU cc_start: 0.9692 (mt) cc_final: 0.9462 (mt) REVERT: K 120 PHE cc_start: 0.6443 (m-80) cc_final: 0.6199 (m-10) outliers start: 0 outliers final: 0 residues processed: 561 average time/residue: 0.7280 time to fit residues: 656.2435 Evaluate side-chains 475 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 475 time to evaluate : 3.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 126 optimal weight: 0.6980 chunk 338 optimal weight: 40.0000 chunk 74 optimal weight: 7.9990 chunk 220 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 376 optimal weight: 60.0000 chunk 312 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 31560 Z= 0.349 Angle : 0.621 7.242 43205 Z= 0.349 Chirality : 0.040 0.162 4991 Planarity : 0.005 0.050 5289 Dihedral : 16.195 145.277 5254 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 26.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.60 % Favored : 89.34 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: -2.15 (0.14), residues: 3368 helix: -1.07 (0.14), residues: 1162 sheet: -1.78 (0.22), residues: 506 loop : -1.48 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 656 HIS 0.009 0.002 HIS A 80 PHE 0.030 0.002 PHE H 6 TYR 0.020 0.002 TYR E 28 ARG 0.011 0.001 ARG B 605 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 542 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 542 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9583 (tp40) cc_final: 0.9317 (tm-30) REVERT: A 95 PHE cc_start: 0.9484 (m-10) cc_final: 0.9172 (m-10) REVERT: A 211 PHE cc_start: 0.9559 (m-10) cc_final: 0.9208 (m-10) REVERT: A 234 MET cc_start: 0.9693 (mtp) cc_final: 0.9269 (mtp) REVERT: A 326 ARG cc_start: 0.9641 (tmm-80) cc_final: 0.8972 (tmm-80) REVERT: A 444 PHE cc_start: 0.8898 (m-10) cc_final: 0.8574 (m-80) REVERT: A 487 MET cc_start: 0.8910 (ttm) cc_final: 0.8108 (ttm) REVERT: A 504 LEU cc_start: 0.9409 (mt) cc_final: 0.9132 (mt) REVERT: A 619 LYS cc_start: 0.9316 (tttt) cc_final: 0.9103 (ttmm) REVERT: A 676 MET cc_start: 0.9614 (mmt) cc_final: 0.9258 (mmm) REVERT: A 764 CYS cc_start: 0.7868 (p) cc_final: 0.7643 (p) REVERT: A 784 LEU cc_start: 0.9303 (mt) cc_final: 0.9043 (mt) REVERT: A 846 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8776 (tm-30) REVERT: A 848 ILE cc_start: 0.9654 (mm) cc_final: 0.9429 (mm) REVERT: A 1048 ASN cc_start: 0.9499 (t0) cc_final: 0.9062 (t0) REVERT: A 1285 MET cc_start: 0.8658 (mmp) cc_final: 0.8159 (mmm) REVERT: A 1334 ASP cc_start: 0.9571 (m-30) cc_final: 0.9111 (m-30) REVERT: A 1336 MET cc_start: 0.9611 (ttp) cc_final: 0.9084 (tmm) REVERT: A 1372 VAL cc_start: 0.9454 (m) cc_final: 0.9171 (m) REVERT: A 1375 MET cc_start: 0.9381 (mtp) cc_final: 0.9172 (mtp) REVERT: B 34 ILE cc_start: 0.9723 (mp) cc_final: 0.9470 (mp) REVERT: B 38 PHE cc_start: 0.9438 (m-80) cc_final: 0.9114 (m-80) REVERT: B 236 HIS cc_start: 0.8995 (p-80) cc_final: 0.8716 (p-80) REVERT: B 452 THR cc_start: 0.9041 (m) cc_final: 0.8831 (p) REVERT: B 484 ASN cc_start: 0.9121 (t0) cc_final: 0.8894 (t0) REVERT: B 597 MET cc_start: 0.9466 (tpt) cc_final: 0.9259 (tpp) REVERT: B 834 ASN cc_start: 0.9359 (p0) cc_final: 0.8969 (p0) REVERT: B 860 MET cc_start: 0.8874 (ppp) cc_final: 0.8380 (ppp) REVERT: B 946 ASN cc_start: 0.8344 (t0) cc_final: 0.7753 (p0) REVERT: B 969 ARG cc_start: 0.7543 (ptt180) cc_final: 0.6920 (ptt180) REVERT: B 980 PHE cc_start: 0.8462 (m-10) cc_final: 0.8077 (m-10) REVERT: B 1098 MET cc_start: 0.9099 (mmp) cc_final: 0.8540 (mmm) REVERT: B 1149 GLU cc_start: 0.9289 (tm-30) cc_final: 0.8695 (tm-30) REVERT: B 1158 PHE cc_start: 0.8670 (t80) cc_final: 0.8328 (t80) REVERT: C 61 GLU cc_start: 0.8981 (mp0) cc_final: 0.8469 (mp0) REVERT: F 120 ILE cc_start: 0.8800 (mt) cc_final: 0.8264 (tp) REVERT: H 40 LEU cc_start: 0.9078 (tp) cc_final: 0.8209 (tp) REVERT: H 46 LEU cc_start: 0.9078 (mt) cc_final: 0.8840 (mt) REVERT: H 122 LEU cc_start: 0.9378 (mt) cc_final: 0.9030 (mt) REVERT: I 111 THR cc_start: 0.9008 (p) cc_final: 0.8548 (t) REVERT: K 120 PHE cc_start: 0.6615 (m-80) cc_final: 0.6398 (m-10) REVERT: L 46 VAL cc_start: 0.7478 (m) cc_final: 0.7061 (t) REVERT: L 56 LEU cc_start: 0.9539 (mt) cc_final: 0.9215 (mp) outliers start: 0 outliers final: 0 residues processed: 542 average time/residue: 0.7272 time to fit residues: 634.9903 Evaluate side-chains 464 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 464 time to evaluate : 3.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 362 optimal weight: 40.0000 chunk 42 optimal weight: 0.6980 chunk 214 optimal weight: 0.8980 chunk 274 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 316 optimal weight: 6.9990 chunk 210 optimal weight: 0.0020 chunk 374 optimal weight: 50.0000 chunk 234 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 overall best weight: 1.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 GLN ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31560 Z= 0.215 Angle : 0.548 12.948 43205 Z= 0.301 Chirality : 0.039 0.156 4991 Planarity : 0.004 0.059 5289 Dihedral : 16.096 140.826 5254 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.30 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: -1.68 (0.14), residues: 3368 helix: -0.57 (0.15), residues: 1155 sheet: -1.76 (0.22), residues: 514 loop : -1.20 (0.15), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 656 HIS 0.008 0.001 HIS A 80 PHE 0.035 0.002 PHE B 377 TYR 0.015 0.001 TYR E 28 ARG 0.011 0.001 ARG B 605 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 561 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 561 time to evaluate : 3.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9555 (tp40) cc_final: 0.9302 (tm-30) REVERT: A 281 HIS cc_start: 0.9340 (t-90) cc_final: 0.8992 (t-90) REVERT: A 326 ARG cc_start: 0.9607 (tmm-80) cc_final: 0.8943 (tmm-80) REVERT: A 444 PHE cc_start: 0.8842 (m-10) cc_final: 0.8467 (m-10) REVERT: A 487 MET cc_start: 0.8850 (ttm) cc_final: 0.8032 (ttm) REVERT: A 504 LEU cc_start: 0.9375 (mt) cc_final: 0.9121 (mt) REVERT: A 619 LYS cc_start: 0.9311 (tttt) cc_final: 0.9090 (ttmm) REVERT: A 676 MET cc_start: 0.9606 (mmt) cc_final: 0.9236 (mmm) REVERT: A 734 GLU cc_start: 0.9413 (tm-30) cc_final: 0.9172 (tp30) REVERT: A 764 CYS cc_start: 0.8007 (p) cc_final: 0.7757 (p) REVERT: A 784 LEU cc_start: 0.9302 (mt) cc_final: 0.9038 (mt) REVERT: A 846 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8633 (tm-30) REVERT: A 1048 ASN cc_start: 0.9491 (t0) cc_final: 0.8977 (t0) REVERT: A 1209 MET cc_start: 0.8337 (ttt) cc_final: 0.7607 (ttm) REVERT: A 1285 MET cc_start: 0.8594 (mmp) cc_final: 0.8073 (mmm) REVERT: A 1334 ASP cc_start: 0.9454 (m-30) cc_final: 0.9098 (m-30) REVERT: A 1372 VAL cc_start: 0.9385 (m) cc_final: 0.9132 (m) REVERT: A 1375 MET cc_start: 0.9347 (mtp) cc_final: 0.9146 (mtp) REVERT: B 34 ILE cc_start: 0.9709 (mp) cc_final: 0.9466 (mp) REVERT: B 38 PHE cc_start: 0.9411 (m-80) cc_final: 0.9031 (m-80) REVERT: B 236 HIS cc_start: 0.8953 (p-80) cc_final: 0.8628 (p-80) REVERT: B 432 MET cc_start: 0.8303 (ttt) cc_final: 0.7725 (ttm) REVERT: B 444 MET cc_start: 0.7584 (mpp) cc_final: 0.7367 (pmm) REVERT: B 696 GLU cc_start: 0.9523 (mm-30) cc_final: 0.9268 (mm-30) REVERT: B 834 ASN cc_start: 0.9344 (p0) cc_final: 0.8960 (p0) REVERT: B 860 MET cc_start: 0.8867 (ppp) cc_final: 0.8448 (ppp) REVERT: B 946 ASN cc_start: 0.8379 (t0) cc_final: 0.7708 (p0) REVERT: B 969 ARG cc_start: 0.7475 (ptt180) cc_final: 0.6616 (ptt180) REVERT: B 980 PHE cc_start: 0.8380 (m-10) cc_final: 0.8026 (m-10) REVERT: B 1098 MET cc_start: 0.9103 (mmp) cc_final: 0.8514 (mmm) REVERT: B 1149 GLU cc_start: 0.9286 (tm-30) cc_final: 0.8632 (tm-30) REVERT: B 1158 PHE cc_start: 0.8581 (t80) cc_final: 0.8121 (t80) REVERT: C 61 GLU cc_start: 0.8959 (mp0) cc_final: 0.8354 (mp0) REVERT: F 120 ILE cc_start: 0.8734 (mt) cc_final: 0.8179 (tp) REVERT: H 46 LEU cc_start: 0.9082 (mt) cc_final: 0.8842 (mt) REVERT: H 123 MET cc_start: 0.9091 (mmp) cc_final: 0.8747 (mmp) REVERT: I 86 PHE cc_start: 0.9687 (p90) cc_final: 0.9248 (p90) REVERT: I 101 PHE cc_start: 0.9089 (m-80) cc_final: 0.8718 (m-80) REVERT: I 111 THR cc_start: 0.8919 (p) cc_final: 0.8532 (t) REVERT: J 32 GLU cc_start: 0.9393 (mm-30) cc_final: 0.9166 (mm-30) REVERT: J 36 LEU cc_start: 0.9675 (mt) cc_final: 0.9452 (mt) REVERT: K 120 PHE cc_start: 0.6502 (m-80) cc_final: 0.6287 (m-10) REVERT: L 46 VAL cc_start: 0.7491 (m) cc_final: 0.7011 (t) REVERT: L 56 LEU cc_start: 0.9525 (mt) cc_final: 0.9196 (mp) outliers start: 0 outliers final: 0 residues processed: 561 average time/residue: 0.7376 time to fit residues: 664.3541 Evaluate side-chains 473 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 473 time to evaluate : 3.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 231 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 238 optimal weight: 3.9990 chunk 255 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 ASN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN H 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31560 Z= 0.261 Angle : 0.559 6.395 43205 Z= 0.310 Chirality : 0.039 0.164 4991 Planarity : 0.004 0.054 5289 Dihedral : 16.069 141.806 5254 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.59 % Favored : 90.35 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: -1.75 (0.14), residues: 3368 helix: -0.62 (0.15), residues: 1158 sheet: -1.71 (0.23), residues: 495 loop : -1.30 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 552 HIS 0.008 0.001 HIS A 80 PHE 0.022 0.002 PHE H 6 TYR 0.016 0.002 TYR E 28 ARG 0.010 0.001 ARG B 605 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 551 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 551 time to evaluate : 3.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9543 (tp40) cc_final: 0.9302 (tm-30) REVERT: A 95 PHE cc_start: 0.9471 (m-10) cc_final: 0.9255 (m-10) REVERT: A 281 HIS cc_start: 0.9342 (t-90) cc_final: 0.8999 (t-90) REVERT: A 326 ARG cc_start: 0.9605 (tmm-80) cc_final: 0.8960 (tmm-80) REVERT: A 444 PHE cc_start: 0.8903 (m-10) cc_final: 0.8472 (m-10) REVERT: A 487 MET cc_start: 0.8907 (ttm) cc_final: 0.8015 (ttm) REVERT: A 504 LEU cc_start: 0.9394 (mt) cc_final: 0.9135 (mt) REVERT: A 619 LYS cc_start: 0.9317 (tttt) cc_final: 0.9101 (ttmm) REVERT: A 676 MET cc_start: 0.9586 (mmt) cc_final: 0.9206 (mmm) REVERT: A 734 GLU cc_start: 0.9390 (tm-30) cc_final: 0.9150 (tp30) REVERT: A 764 CYS cc_start: 0.7993 (p) cc_final: 0.7729 (p) REVERT: A 784 LEU cc_start: 0.9291 (mt) cc_final: 0.9036 (mt) REVERT: A 846 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8670 (tm-30) REVERT: A 1048 ASN cc_start: 0.9485 (t0) cc_final: 0.9055 (t0) REVERT: A 1285 MET cc_start: 0.8653 (mmp) cc_final: 0.8139 (mmm) REVERT: A 1334 ASP cc_start: 0.9546 (m-30) cc_final: 0.9337 (m-30) REVERT: A 1372 VAL cc_start: 0.9440 (m) cc_final: 0.9153 (m) REVERT: A 1375 MET cc_start: 0.9354 (mtp) cc_final: 0.9127 (mtp) REVERT: B 34 ILE cc_start: 0.9716 (mp) cc_final: 0.9488 (mp) REVERT: B 38 PHE cc_start: 0.9434 (m-80) cc_final: 0.9039 (m-80) REVERT: B 236 HIS cc_start: 0.8935 (p-80) cc_final: 0.8599 (p-80) REVERT: B 458 LYS cc_start: 0.9531 (pptt) cc_final: 0.9326 (ptmm) REVERT: B 484 ASN cc_start: 0.8838 (t0) cc_final: 0.8424 (t0) REVERT: B 834 ASN cc_start: 0.9368 (p0) cc_final: 0.8989 (p0) REVERT: B 946 ASN cc_start: 0.8377 (t0) cc_final: 0.7688 (p0) REVERT: B 969 ARG cc_start: 0.7507 (ptt180) cc_final: 0.6645 (ptt180) REVERT: B 980 PHE cc_start: 0.8282 (m-10) cc_final: 0.8022 (m-10) REVERT: B 997 GLU cc_start: 0.9491 (pm20) cc_final: 0.9291 (pm20) REVERT: B 1098 MET cc_start: 0.9127 (mmp) cc_final: 0.8521 (mmm) REVERT: B 1149 GLU cc_start: 0.9282 (tm-30) cc_final: 0.8625 (tm-30) REVERT: B 1158 PHE cc_start: 0.8617 (t80) cc_final: 0.8312 (t80) REVERT: C 61 GLU cc_start: 0.8966 (mp0) cc_final: 0.8362 (mp0) REVERT: F 120 ILE cc_start: 0.8765 (mt) cc_final: 0.8211 (tp) REVERT: H 46 LEU cc_start: 0.9099 (mt) cc_final: 0.8883 (mt) REVERT: H 123 MET cc_start: 0.8927 (mmp) cc_final: 0.8713 (mmm) REVERT: I 86 PHE cc_start: 0.9691 (p90) cc_final: 0.9250 (p90) REVERT: I 101 PHE cc_start: 0.9023 (m-80) cc_final: 0.8690 (m-80) REVERT: I 111 THR cc_start: 0.8995 (p) cc_final: 0.8613 (t) REVERT: J 32 GLU cc_start: 0.9435 (mm-30) cc_final: 0.9211 (mm-30) REVERT: K 120 PHE cc_start: 0.6504 (m-80) cc_final: 0.6292 (m-10) REVERT: L 46 VAL cc_start: 0.7456 (m) cc_final: 0.6964 (t) REVERT: L 56 LEU cc_start: 0.9517 (mt) cc_final: 0.9197 (mp) outliers start: 0 outliers final: 0 residues processed: 551 average time/residue: 0.7693 time to fit residues: 683.0015 Evaluate side-chains 472 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 472 time to evaluate : 3.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 341 optimal weight: 50.0000 chunk 359 optimal weight: 40.0000 chunk 327 optimal weight: 0.0670 chunk 349 optimal weight: 80.0000 chunk 210 optimal weight: 9.9990 chunk 152 optimal weight: 4.9990 chunk 274 optimal weight: 0.1980 chunk 107 optimal weight: 3.9990 chunk 315 optimal weight: 6.9990 chunk 330 optimal weight: 4.9990 chunk 348 optimal weight: 40.0000 overall best weight: 2.8524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN H 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 31560 Z= 0.307 Angle : 0.595 8.204 43205 Z= 0.332 Chirality : 0.040 0.306 4991 Planarity : 0.005 0.058 5289 Dihedral : 16.101 142.247 5254 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 24.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.95 % Favored : 89.99 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: -1.97 (0.14), residues: 3368 helix: -0.80 (0.14), residues: 1155 sheet: -1.81 (0.22), residues: 495 loop : -1.44 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 656 HIS 0.017 0.002 HIS A1124 PHE 0.033 0.002 PHE A 655 TYR 0.017 0.002 TYR E 28 ARG 0.010 0.001 ARG B 605 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 539 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 539 time to evaluate : 3.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9549 (tp40) cc_final: 0.9321 (tm-30) REVERT: A 281 HIS cc_start: 0.9333 (t-90) cc_final: 0.8998 (t-90) REVERT: A 326 ARG cc_start: 0.9610 (tmm-80) cc_final: 0.8965 (tmm-80) REVERT: A 444 PHE cc_start: 0.8976 (m-10) cc_final: 0.8473 (m-10) REVERT: A 487 MET cc_start: 0.8900 (ttm) cc_final: 0.8096 (ttm) REVERT: A 504 LEU cc_start: 0.9390 (mt) cc_final: 0.9143 (mt) REVERT: A 586 ILE cc_start: 0.9647 (mm) cc_final: 0.9437 (mt) REVERT: A 619 LYS cc_start: 0.9316 (tttt) cc_final: 0.9094 (ttmm) REVERT: A 676 MET cc_start: 0.9577 (mmt) cc_final: 0.9210 (mmm) REVERT: A 734 GLU cc_start: 0.9403 (tm-30) cc_final: 0.9152 (tp30) REVERT: A 764 CYS cc_start: 0.7860 (p) cc_final: 0.7617 (p) REVERT: A 784 LEU cc_start: 0.9246 (mt) cc_final: 0.8986 (mt) REVERT: A 846 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8745 (tm-30) REVERT: A 848 ILE cc_start: 0.9659 (mm) cc_final: 0.9426 (mm) REVERT: A 1048 ASN cc_start: 0.9500 (t0) cc_final: 0.9071 (t0) REVERT: A 1209 MET cc_start: 0.8354 (ttt) cc_final: 0.7597 (ttm) REVERT: A 1285 MET cc_start: 0.8589 (mmp) cc_final: 0.8115 (mmm) REVERT: A 1334 ASP cc_start: 0.9586 (m-30) cc_final: 0.9261 (m-30) REVERT: A 1372 VAL cc_start: 0.9440 (m) cc_final: 0.9145 (m) REVERT: A 1375 MET cc_start: 0.9373 (mtp) cc_final: 0.9151 (mtp) REVERT: B 34 ILE cc_start: 0.9723 (mp) cc_final: 0.9487 (mp) REVERT: B 38 PHE cc_start: 0.9444 (m-80) cc_final: 0.9069 (m-80) REVERT: B 236 HIS cc_start: 0.8958 (p-80) cc_final: 0.8586 (p-80) REVERT: B 484 ASN cc_start: 0.8847 (t0) cc_final: 0.8430 (t0) REVERT: B 696 GLU cc_start: 0.9512 (mm-30) cc_final: 0.9279 (mm-30) REVERT: B 834 ASN cc_start: 0.9375 (p0) cc_final: 0.9013 (p0) REVERT: B 946 ASN cc_start: 0.8366 (t0) cc_final: 0.7686 (p0) REVERT: B 969 ARG cc_start: 0.7635 (ptt180) cc_final: 0.6803 (ptt180) REVERT: B 980 PHE cc_start: 0.8334 (m-10) cc_final: 0.7971 (m-10) REVERT: B 997 GLU cc_start: 0.9460 (pm20) cc_final: 0.9253 (pm20) REVERT: B 1098 MET cc_start: 0.9181 (mmp) cc_final: 0.8595 (mmm) REVERT: B 1133 MET cc_start: 0.9209 (mmm) cc_final: 0.8984 (mmm) REVERT: B 1149 GLU cc_start: 0.9291 (tm-30) cc_final: 0.8629 (tm-30) REVERT: B 1158 PHE cc_start: 0.8642 (t80) cc_final: 0.8332 (t80) REVERT: C 61 GLU cc_start: 0.8973 (mp0) cc_final: 0.8382 (mp0) REVERT: H 46 LEU cc_start: 0.9131 (mt) cc_final: 0.8923 (mt) REVERT: I 86 PHE cc_start: 0.9695 (p90) cc_final: 0.9300 (p90) REVERT: I 101 PHE cc_start: 0.9013 (m-80) cc_final: 0.8691 (m-80) REVERT: I 111 THR cc_start: 0.8979 (p) cc_final: 0.8593 (t) REVERT: K 120 PHE cc_start: 0.6616 (m-80) cc_final: 0.6414 (m-10) REVERT: L 46 VAL cc_start: 0.7513 (m) cc_final: 0.7013 (t) REVERT: L 56 LEU cc_start: 0.9528 (mt) cc_final: 0.9218 (mp) outliers start: 0 outliers final: 0 residues processed: 539 average time/residue: 0.7299 time to fit residues: 636.7468 Evaluate side-chains 460 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 460 time to evaluate : 3.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 229 optimal weight: 0.7980 chunk 369 optimal weight: 60.0000 chunk 225 optimal weight: 0.0980 chunk 175 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 chunk 387 optimal weight: 3.9990 chunk 356 optimal weight: 50.0000 chunk 308 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 238 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31560 Z= 0.170 Angle : 0.526 7.648 43205 Z= 0.287 Chirality : 0.040 0.189 4991 Planarity : 0.004 0.051 5289 Dihedral : 15.994 138.203 5254 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.77 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: -1.34 (0.14), residues: 3368 helix: -0.18 (0.15), residues: 1156 sheet: -1.74 (0.22), residues: 509 loop : -1.03 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 552 HIS 0.012 0.001 HIS B 984 PHE 0.023 0.002 PHE A 655 TYR 0.013 0.001 TYR E 28 ARG 0.022 0.001 ARG A 344 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 105 is missing expected H atoms. Skipping. Evaluate side-chains 562 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 562 time to evaluate : 3.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9534 (tp40) cc_final: 0.9301 (tm-30) REVERT: A 95 PHE cc_start: 0.9441 (m-10) cc_final: 0.9227 (m-10) REVERT: A 281 HIS cc_start: 0.9293 (t-90) cc_final: 0.8946 (t-90) REVERT: A 326 ARG cc_start: 0.9591 (tmm-80) cc_final: 0.8926 (tmm-80) REVERT: A 444 PHE cc_start: 0.8879 (m-10) cc_final: 0.8392 (m-10) REVERT: A 487 MET cc_start: 0.8851 (ttm) cc_final: 0.7943 (ttm) REVERT: A 504 LEU cc_start: 0.9379 (mt) cc_final: 0.9137 (mt) REVERT: A 586 ILE cc_start: 0.9645 (mm) cc_final: 0.9439 (mt) REVERT: A 619 LYS cc_start: 0.9290 (tttt) cc_final: 0.9063 (ttmm) REVERT: A 676 MET cc_start: 0.9571 (mmt) cc_final: 0.9188 (mmm) REVERT: A 734 GLU cc_start: 0.9385 (tm-30) cc_final: 0.9139 (tp30) REVERT: A 784 LEU cc_start: 0.9250 (mt) cc_final: 0.9043 (mt) REVERT: A 846 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8759 (tm-30) REVERT: A 956 LEU cc_start: 0.9594 (mt) cc_final: 0.9361 (mp) REVERT: A 1048 ASN cc_start: 0.9465 (t0) cc_final: 0.8976 (t0) REVERT: A 1209 MET cc_start: 0.8310 (ttt) cc_final: 0.7520 (ttm) REVERT: A 1267 MET cc_start: 0.9504 (mpp) cc_final: 0.9077 (ppp) REVERT: A 1268 LEU cc_start: 0.9602 (mt) cc_final: 0.8993 (mt) REVERT: A 1284 MET cc_start: 0.8811 (mtt) cc_final: 0.8597 (mtt) REVERT: A 1285 MET cc_start: 0.8532 (mmp) cc_final: 0.8078 (mmm) REVERT: A 1334 ASP cc_start: 0.9539 (m-30) cc_final: 0.9197 (m-30) REVERT: A 1365 TYR cc_start: 0.9138 (t80) cc_final: 0.8211 (t80) REVERT: A 1372 VAL cc_start: 0.9383 (m) cc_final: 0.9131 (m) REVERT: A 1375 MET cc_start: 0.9348 (mtp) cc_final: 0.9083 (mtp) REVERT: B 34 ILE cc_start: 0.9707 (mp) cc_final: 0.9469 (mp) REVERT: B 38 PHE cc_start: 0.9435 (m-80) cc_final: 0.9060 (m-80) REVERT: B 199 MET cc_start: 0.9066 (mmp) cc_final: 0.8647 (mmp) REVERT: B 312 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8498 (tm-30) REVERT: B 432 MET cc_start: 0.8364 (ttt) cc_final: 0.7800 (ttm) REVERT: B 484 ASN cc_start: 0.8860 (t0) cc_final: 0.8449 (t0) REVERT: B 834 ASN cc_start: 0.9350 (p0) cc_final: 0.8959 (p0) REVERT: B 860 MET cc_start: 0.8882 (ppp) cc_final: 0.8368 (ppp) REVERT: B 946 ASN cc_start: 0.8363 (t0) cc_final: 0.7672 (p0) REVERT: B 969 ARG cc_start: 0.7241 (ptt180) cc_final: 0.6532 (ptt180) REVERT: B 980 PHE cc_start: 0.8300 (m-10) cc_final: 0.7984 (m-10) REVERT: B 997 GLU cc_start: 0.9562 (pm20) cc_final: 0.9260 (pm20) REVERT: B 1098 MET cc_start: 0.9165 (mmp) cc_final: 0.8532 (mmm) REVERT: B 1149 GLU cc_start: 0.9264 (tm-30) cc_final: 0.8581 (tm-30) REVERT: B 1158 PHE cc_start: 0.8552 (t80) cc_final: 0.8227 (t80) REVERT: C 61 GLU cc_start: 0.8904 (mp0) cc_final: 0.8366 (mp0) REVERT: F 86 THR cc_start: 0.9236 (m) cc_final: 0.9001 (m) REVERT: H 1 MET cc_start: 0.3753 (mmm) cc_final: 0.3325 (tpt) REVERT: H 123 MET cc_start: 0.8957 (mmp) cc_final: 0.8650 (mmm) REVERT: I 86 PHE cc_start: 0.9669 (p90) cc_final: 0.9205 (p90) REVERT: I 101 PHE cc_start: 0.8988 (m-80) cc_final: 0.8677 (m-80) REVERT: I 111 THR cc_start: 0.8994 (p) cc_final: 0.8652 (t) REVERT: J 36 LEU cc_start: 0.9605 (mt) cc_final: 0.9385 (mt) REVERT: K 120 PHE cc_start: 0.6470 (m-80) cc_final: 0.6259 (m-10) REVERT: L 46 VAL cc_start: 0.7273 (m) cc_final: 0.6779 (t) REVERT: L 56 LEU cc_start: 0.9495 (mt) cc_final: 0.9187 (mp) outliers start: 0 outliers final: 0 residues processed: 562 average time/residue: 0.7394 time to fit residues: 670.0256 Evaluate side-chains 480 residues out of total 3003 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 3.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 245 optimal weight: 2.9990 chunk 328 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 284 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 309 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 317 optimal weight: 4.9990 chunk 39 optimal weight: 40.0000 chunk 56 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN H 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.086737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.060176 restraints weight = 388367.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.063128 restraints weight = 187005.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.065183 restraints weight = 111036.764| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31560 Z= 0.215 Angle : 0.528 6.349 43205 Z= 0.292 Chirality : 0.039 0.173 4991 Planarity : 0.004 0.047 5289 Dihedral : 15.961 140.180 5254 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.02 % Favored : 91.92 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % 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: -1.34 (0.14), residues: 3368 helix: -0.18 (0.15), residues: 1154 sheet: -1.69 (0.23), residues: 498 loop : -1.05 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 552 HIS 0.008 0.001 HIS A1124 PHE 0.022 0.002 PHE A 655 TYR 0.015 0.001 TYR E 28 ARG 0.010 0.001 ARG A 344 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11972.38 seconds wall clock time: 207 minutes 47.58 seconds (12467.58 seconds total)