Starting phenix.real_space_refine on Sun Aug 24 00:17:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qbj_53000/08_2025/9qbj_53000.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qbj_53000/08_2025/9qbj_53000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qbj_53000/08_2025/9qbj_53000.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qbj_53000/08_2025/9qbj_53000.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qbj_53000/08_2025/9qbj_53000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qbj_53000/08_2025/9qbj_53000.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.014 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 9886 2.51 5 N 2602 2.21 5 O 3050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15600 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 1036 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 3, 'TRANS': 127} Conformer: "B" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 3, 'TRANS': 127} bond proxies already assigned to first conformer: 1016 Chain: "D" Number of atoms: 1046 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 1027 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 132, 1027 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 3, 'TRANS': 128} bond proxies already assigned to first conformer: 1027 Chain: "E" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1582 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 14, 'TRANS': 192} Chain breaks: 2 Chain: "F" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1588 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain breaks: 2 Chain: "G" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1582 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 14, 'TRANS': 192} Chain breaks: 2 Chain: "H" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1588 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain breaks: 2 Chain: "I" Number of atoms: 3781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3781 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 26, 'TRANS': 457} Chain breaks: 7 Chain: "J" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3351 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 21, 'TRANS': 406} Chain breaks: 7 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ASER C 23 " occ=0.80 ... (10 atoms not shown) pdb=" OG BSER C 23 " occ=0.20 residue: pdb=" N ATHR C 25 " occ=0.80 ... (12 atoms not shown) pdb=" CG2BTHR C 25 " occ=0.20 residue: pdb=" N ASER C 27 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 27 " occ=0.50 residue: pdb=" N ASER D 23 " occ=0.80 ... (10 atoms not shown) pdb=" OG BSER D 23 " occ=0.20 residue: pdb=" N ATHR D 25 " occ=0.80 ... (12 atoms not shown) pdb=" CG2BTHR D 25 " occ=0.20 residue: pdb=" N ASER D 27 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 27 " occ=0.50 Time building chain proxies: 3.96, per 1000 atoms: 0.25 Number of scatterers: 15600 At special positions: 0 Unit cell: (135.196, 142.604, 150.012, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 3050 8.00 N 2602 7.00 C 9886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 100 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 206 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 94 " distance=2.04 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 199 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 150 " - pdb=" SG CYS G 206 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 94 " distance=2.04 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 199 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " BGC A 1 " - " GLC A 2 " " BGC B 1 " - " GLC B 2 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 785.4 milliseconds Enol-peptide restraints added in 2.1 microseconds 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3722 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 38 sheets defined 31.0% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'C' and resid 30 through 36 Processing helix chain 'C' and resid 66 through 69 Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'D' and resid 30 through 36 Processing helix chain 'D' and resid 91 through 95 removed outlier: 3.671A pdb=" N THR D 95 " --> pdb=" O PRO D 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.554A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.892A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'F' and resid 126 through 132 Processing helix chain 'F' and resid 188 through 194 removed outlier: 3.569A pdb=" N HIS F 194 " --> pdb=" O ASP F 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.751A pdb=" N PHE G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.823A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 107 Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'H' and resid 85 through 89 removed outlier: 3.841A pdb=" N LEU H 89 " --> pdb=" O PRO H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 133 Processing helix chain 'H' and resid 188 through 194 removed outlier: 3.660A pdb=" N HIS H 194 " --> pdb=" O ASP H 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 36 Processing helix chain 'I' and resid 51 through 60 Proline residue: I 57 - end of helix Processing helix chain 'I' and resid 73 through 82 removed outlier: 3.869A pdb=" N GLY I 77 " --> pdb=" O HIS I 73 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY I 78 " --> pdb=" O ASP I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 98 removed outlier: 3.811A pdb=" N LEU I 98 " --> pdb=" O PHE I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 106 removed outlier: 3.614A pdb=" N TRP I 103 " --> pdb=" O TYR I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 149 Processing helix chain 'I' and resid 162 through 173 removed outlier: 3.818A pdb=" N THR I 166 " --> pdb=" O GLU I 162 " (cutoff:3.500A) Proline residue: I 168 - end of helix removed outlier: 4.317A pdb=" N ASP I 173 " --> pdb=" O LEU I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 210 Processing helix chain 'I' and resid 218 through 228 Processing helix chain 'I' and resid 239 through 246 removed outlier: 4.383A pdb=" N ASN I 243 " --> pdb=" O TRP I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 292 Processing helix chain 'I' and resid 295 through 306 Processing helix chain 'I' and resid 313 through 321 Processing helix chain 'I' and resid 323 through 336 Processing helix chain 'I' and resid 344 through 361 removed outlier: 3.919A pdb=" N PHE I 348 " --> pdb=" O GLN I 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 378 removed outlier: 3.946A pdb=" N MET I 378 " --> pdb=" O GLN I 374 " (cutoff:3.500A) Processing helix chain 'I' and resid 382 through 396 Processing helix chain 'I' and resid 399 through 414 Processing helix chain 'I' and resid 425 through 437 removed outlier: 3.745A pdb=" N SER I 430 " --> pdb=" O GLY I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 442 through 456 Processing helix chain 'I' and resid 459 through 474 Processing helix chain 'I' and resid 510 through 525 Processing helix chain 'J' and resid 73 through 83 removed outlier: 4.129A pdb=" N GLY J 77 " --> pdb=" O HIS J 73 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY J 78 " --> pdb=" O ASP J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 98 Processing helix chain 'J' and resid 99 through 106 removed outlier: 3.526A pdb=" N TRP J 103 " --> pdb=" O TYR J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 149 removed outlier: 4.504A pdb=" N ALA J 143 " --> pdb=" O GLU J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 173 removed outlier: 4.015A pdb=" N THR J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) Proline residue: J 168 - end of helix removed outlier: 4.275A pdb=" N ASP J 173 " --> pdb=" O LEU J 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 210 Processing helix chain 'J' and resid 218 through 228 Processing helix chain 'J' and resid 239 through 247 removed outlier: 4.477A pdb=" N ASN J 243 " --> pdb=" O TRP J 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 292 Processing helix chain 'J' and resid 295 through 306 removed outlier: 3.608A pdb=" N ASP J 305 " --> pdb=" O ALA J 301 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 321 Processing helix chain 'J' and resid 323 through 336 Processing helix chain 'J' and resid 345 through 362 removed outlier: 3.663A pdb=" N GLY J 362 " --> pdb=" O ASN J 358 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 378 Processing helix chain 'J' and resid 382 through 396 Processing helix chain 'J' and resid 399 through 414 Processing helix chain 'J' and resid 429 through 436 removed outlier: 3.786A pdb=" N LEU J 436 " --> pdb=" O PHE J 432 " (cutoff:3.500A) Processing helix chain 'J' and resid 442 through 456 Processing helix chain 'J' and resid 459 through 475 removed outlier: 3.605A pdb=" N GLY J 465 " --> pdb=" O THR J 461 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER J 473 " --> pdb=" O LYS J 469 " (cutoff:3.500A) Processing helix chain 'J' and resid 510 through 525 Processing sheet with id=AA1, first strand: chain 'C' and resid 5 through 9 Processing sheet with id=AA2, first strand: chain 'C' and resid 12 through 14 removed outlier: 6.108A pdb=" N GLY C 12 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N MET C 39 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA C 55 " --> pdb=" O MET C 39 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP C 41 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 12 through 14 removed outlier: 6.108A pdb=" N GLY C 12 " --> pdb=" O THR C 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 5 through 9 Processing sheet with id=AA5, first strand: chain 'D' and resid 12 through 14 removed outlier: 6.434A pdb=" N ARG D 43 " --> pdb=" O MET D 52 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N MET D 52 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 12 through 14 Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.915A pdb=" N GLY E 33 " --> pdb=" O ARG E 99 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.433A pdb=" N TYR E 112 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 130 through 134 removed outlier: 4.321A pdb=" N GLY E 149 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR E 186 " --> pdb=" O ASP E 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 130 through 134 removed outlier: 4.321A pdb=" N GLY E 149 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR E 186 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER E 187 " --> pdb=" O VAL E 179 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 161 through 164 removed outlier: 3.603A pdb=" N LYS E 216 " --> pdb=" O GLU I 503 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS I 501 " --> pdb=" O ASP E 218 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N PHE I 540 " --> pdb=" O THR I 490 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LYS I 492 " --> pdb=" O PHE I 540 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'F' and resid 11 through 14 removed outlier: 6.246A pdb=" N LEU F 11 " --> pdb=" O GLU F 110 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LYS F 112 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL F 13 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP F 41 " --> pdb=" O LEU F 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 11 through 14 removed outlier: 6.246A pdb=" N LEU F 11 " --> pdb=" O GLU F 110 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LYS F 112 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL F 13 " --> pdb=" O LYS F 112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.604A pdb=" N LYS F 36 " --> pdb=" O TYR F 31 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 119 through 123 removed outlier: 5.852A pdb=" N TYR F 178 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 150 through 154 Processing sheet with id=AC1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.906A pdb=" N GLY G 33 " --> pdb=" O ARG G 99 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA G 40 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU G 45 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 130 through 134 removed outlier: 3.948A pdb=" N GLY G 149 " --> pdb=" O LEU G 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 130 through 134 removed outlier: 3.948A pdb=" N GLY G 149 " --> pdb=" O LEU G 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 161 through 164 removed outlier: 3.904A pdb=" N LYS J 501 " --> pdb=" O ASP G 218 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N PHE J 540 " --> pdb=" O THR J 490 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS J 492 " --> pdb=" O PHE J 540 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL J 542 " --> pdb=" O LYS J 492 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL J 494 " --> pdb=" O VAL J 542 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AC7, first strand: chain 'H' and resid 10 through 14 removed outlier: 6.714A pdb=" N LEU H 11 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LYS H 112 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL H 13 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU H 39 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR H 55 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP H 41 " --> pdb=" O LEU H 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 10 through 14 removed outlier: 6.714A pdb=" N LEU H 11 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N LYS H 112 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL H 13 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR H 102 " --> pdb=" O GLN H 96 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 30 through 31 removed outlier: 3.748A pdb=" N LYS H 36 " --> pdb=" O TYR H 31 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 119 through 123 removed outlier: 5.744A pdb=" N TYR H 178 " --> pdb=" O ASN H 143 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 149 through 154 Processing sheet with id=AD3, first strand: chain 'I' and resid 45 through 47 removed outlier: 6.000A pdb=" N ILE I 18 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL I 17 " --> pdb=" O ILE I 68 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N PHE I 70 " --> pdb=" O VAL I 17 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP I 19 " --> pdb=" O PHE I 70 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N ALA I 72 " --> pdb=" O TRP I 19 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA I 273 " --> pdb=" O PRO I 116 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ILE I 275 " --> pdb=" O ALA I 114 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ALA I 114 " --> pdb=" O ILE I 275 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 45 through 47 removed outlier: 6.000A pdb=" N ILE I 18 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL I 17 " --> pdb=" O ILE I 68 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N PHE I 70 " --> pdb=" O VAL I 17 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP I 19 " --> pdb=" O PHE I 70 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N ALA I 72 " --> pdb=" O TRP I 19 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 107 through 108 Processing sheet with id=AD6, first strand: chain 'I' and resid 233 through 236 Processing sheet with id=AD7, first strand: chain 'I' and resid 179 through 181 removed outlier: 4.027A pdb=" N LYS I 179 " --> pdb=" O ASP I 186 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 68 through 72 removed outlier: 6.246A pdb=" N ALA J 273 " --> pdb=" O PRO J 116 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 68 through 72 Processing sheet with id=AE1, first strand: chain 'J' and resid 233 through 236 Processing sheet with id=AE2, first strand: chain 'J' and resid 179 through 181 removed outlier: 3.973A pdb=" N LYS J 179 " --> pdb=" O ASP J 186 " (cutoff:3.500A) 813 hydrogen bonds defined for protein. 2192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5003 1.34 - 1.46: 3719 1.46 - 1.58: 7126 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 15952 Sorted by residual: bond pdb=" CA ASN J 496 " pdb=" CB ASN J 496 " ideal model delta sigma weight residual 1.526 1.575 -0.049 1.76e-02 3.23e+03 7.66e+00 bond pdb=" N LEU D 125 " pdb=" CA LEU D 125 " ideal model delta sigma weight residual 1.455 1.479 -0.024 1.18e-02 7.18e+03 3.99e+00 bond pdb=" CA ASN F 142 " pdb=" CB ASN F 142 " ideal model delta sigma weight residual 1.535 1.573 -0.038 2.02e-02 2.45e+03 3.54e+00 bond pdb=" C TYR F 145 " pdb=" N PRO F 146 " ideal model delta sigma weight residual 1.334 1.355 -0.021 1.11e-02 8.12e+03 3.52e+00 bond pdb=" C1 BGC B 1 " pdb=" O1 BGC B 1 " ideal model delta sigma weight residual 1.379 1.414 -0.035 2.00e-02 2.50e+03 3.10e+00 ... (remaining 15947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 21092 2.03 - 4.06: 443 4.06 - 6.09: 84 6.09 - 8.12: 19 8.12 - 10.15: 14 Bond angle restraints: 21652 Sorted by residual: angle pdb=" CA ARG H 147 " pdb=" CB ARG H 147 " pdb=" CG ARG H 147 " ideal model delta sigma weight residual 114.10 123.97 -9.87 2.00e+00 2.50e-01 2.44e+01 angle pdb=" CA GLU J 443 " pdb=" CB GLU J 443 " pdb=" CG GLU J 443 " ideal model delta sigma weight residual 114.10 123.28 -9.18 2.00e+00 2.50e-01 2.11e+01 angle pdb=" CB LYS I 136 " pdb=" CG LYS I 136 " pdb=" CD LYS I 136 " ideal model delta sigma weight residual 111.30 121.45 -10.15 2.30e+00 1.89e-01 1.95e+01 angle pdb=" CA LYS E 216 " pdb=" CB LYS E 216 " pdb=" CG LYS E 216 " ideal model delta sigma weight residual 114.10 122.87 -8.77 2.00e+00 2.50e-01 1.92e+01 angle pdb=" CA GLU J 512 " pdb=" CB GLU J 512 " pdb=" CG GLU J 512 " ideal model delta sigma weight residual 114.10 122.42 -8.32 2.00e+00 2.50e-01 1.73e+01 ... (remaining 21647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.93: 8752 22.93 - 45.85: 693 45.85 - 68.78: 88 68.78 - 91.70: 35 91.70 - 114.63: 8 Dihedral angle restraints: 9576 sinusoidal: 3781 harmonic: 5795 Sorted by residual: dihedral pdb=" CB CYS E 150 " pdb=" SG CYS E 150 " pdb=" SG CYS E 206 " pdb=" CB CYS E 206 " ideal model delta sinusoidal sigma weight residual 93.00 140.15 -47.15 1 1.00e+01 1.00e-02 3.07e+01 dihedral pdb=" CB CYS G 150 " pdb=" SG CYS G 150 " pdb=" SG CYS G 206 " pdb=" CB CYS G 206 " ideal model delta sinusoidal sigma weight residual 93.00 138.05 -45.05 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS F 139 " pdb=" SG CYS F 139 " pdb=" SG CYS F 199 " pdb=" CB CYS F 199 " ideal model delta sinusoidal sigma weight residual 93.00 49.94 43.06 1 1.00e+01 1.00e-02 2.59e+01 ... (remaining 9573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2116 0.068 - 0.136: 276 0.136 - 0.204: 10 0.204 - 0.273: 3 0.273 - 0.341: 1 Chirality restraints: 2406 Sorted by residual: chirality pdb=" CB ILE J 495 " pdb=" CA ILE J 495 " pdb=" CG1 ILE J 495 " pdb=" CG2 ILE J 495 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" C5 BGC A 1 " pdb=" C4 BGC A 1 " pdb=" C6 BGC A 1 " pdb=" O5 BGC A 1 " both_signs ideal model delta sigma weight residual False -2.48 -2.23 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA GLU E 158 " pdb=" N GLU E 158 " pdb=" C GLU E 158 " pdb=" CB GLU E 158 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2403 not shown) Planarity restraints: 2776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 124 " -0.024 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" C SER D 124 " 0.082 2.00e-02 2.50e+03 pdb=" O SER D 124 " -0.031 2.00e-02 2.50e+03 pdb=" N LEU D 125 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 89 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.35e+00 pdb=" C ASN D 89 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN D 89 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU D 90 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 214 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C ASN E 214 " -0.044 2.00e-02 2.50e+03 pdb=" O ASN E 214 " 0.017 2.00e-02 2.50e+03 pdb=" N THR E 215 " 0.014 2.00e-02 2.50e+03 ... (remaining 2773 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 595 2.72 - 3.26: 15396 3.26 - 3.81: 25708 3.81 - 4.35: 31482 4.35 - 4.90: 53706 Nonbonded interactions: 126887 Sorted by model distance: nonbonded pdb=" OE1 GLU J 443 " pdb=" ND2 ASN J 447 " model vdw 2.172 3.120 nonbonded pdb=" O ASN J 243 " pdb=" OG1 THR J 246 " model vdw 2.210 3.040 nonbonded pdb=" O ASN I 243 " pdb=" OG1 THR I 246 " model vdw 2.218 3.040 nonbonded pdb=" OE2 GLU J 120 " pdb=" O2 BGC B 1 " model vdw 2.218 3.040 nonbonded pdb=" OE1 GLN D 15 " pdb=" OG1 THR D 128 " model vdw 2.241 3.040 ... (remaining 126882 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 4 through 22 or resid 24 or resid 26 or resid 28 through 1 \ 34)) selection = (chain 'D' and (resid 4 through 22 or resid 24 or resid 26 or resid 28 through 1 \ 34)) } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 66 through 83 or resid 93 through 107 or resid 112 through \ 276 or resid 283 through 416 or resid 428 through 543)) selection = (chain 'J' and (resid 66 through 494 or resid 500 through 543)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.420 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15964 Z= 0.157 Angle : 0.752 10.151 21678 Z= 0.390 Chirality : 0.045 0.341 2406 Planarity : 0.005 0.059 2776 Dihedral : 16.681 114.630 5824 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.24 % Allowed : 18.96 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.19), residues: 1951 helix: 1.10 (0.22), residues: 524 sheet: 0.66 (0.20), residues: 607 loop : -0.08 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 59 TYR 0.016 0.001 TYR F 145 PHE 0.024 0.001 PHE F 144 TRP 0.014 0.001 TRP I 349 HIS 0.004 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00336 (15952) covalent geometry : angle 0.75207 (21652) SS BOND : bond 0.00332 ( 10) SS BOND : angle 0.77299 ( 20) hydrogen bonds : bond 0.13958 ( 762) hydrogen bonds : angle 6.23769 ( 2192) link_ALPHA1-4 : bond 0.01098 ( 2) link_ALPHA1-4 : angle 1.21013 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 230 time to evaluate : 0.629 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: C 58 GLU cc_start: 0.7843 (pp20) cc_final: 0.7291 (pp20) REVERT: C 59 ARG cc_start: 0.8377 (mmm-85) cc_final: 0.8099 (mmm-85) REVERT: C 81 LYS cc_start: 0.7820 (mtmt) cc_final: 0.7288 (mttp) REVERT: C 110 PHE cc_start: 0.9054 (m-10) cc_final: 0.8840 (m-10) REVERT: D 69 GLN cc_start: 0.8663 (tt0) cc_final: 0.8454 (tp40) REVERT: D 116 GLN cc_start: 0.8063 (mp-120) cc_final: 0.7803 (mp10) REVERT: F 110 GLU cc_start: 0.8393 (tp30) cc_final: 0.8037 (tp30) REVERT: F 166 GLU cc_start: 0.8485 (tt0) cc_final: 0.7910 (pp20) REVERT: G 46 GLU cc_start: 0.9038 (pt0) cc_final: 0.8779 (pt0) REVERT: G 103 ASP cc_start: 0.9219 (p0) cc_final: 0.8999 (p0) REVERT: G 216 LYS cc_start: 0.8441 (tppt) cc_final: 0.8235 (tppt) REVERT: G 218 ASP cc_start: 0.8315 (m-30) cc_final: 0.7966 (m-30) REVERT: G 219 LYS cc_start: 0.8576 (tppt) cc_final: 0.8280 (tptm) REVERT: H 175 ASP cc_start: 0.7642 (t0) cc_final: 0.7337 (t0) REVERT: I 446 ARG cc_start: 0.8891 (mtp180) cc_final: 0.8571 (mtm-85) REVERT: J 317 GLU cc_start: 0.6178 (tp30) cc_final: 0.5645 (mm-30) outliers start: 4 outliers final: 1 residues processed: 232 average time/residue: 0.1387 time to fit residues: 45.9134 Evaluate side-chains 195 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 110 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 GLN C 69 GLN C 130 HIS D 89 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS I 182 ASN I 385 GLN I 414 GLN ** I 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 ASN J 250 ASN ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 374 GLN J 445 GLN J 459 GLN J 474 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.114618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.066327 restraints weight = 129145.958| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 6.43 r_work: 0.2800 rms_B_bonded: 5.29 restraints_weight: 2.0000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15964 Z= 0.155 Angle : 0.608 10.307 21678 Z= 0.311 Chirality : 0.042 0.161 2406 Planarity : 0.004 0.040 2776 Dihedral : 6.595 81.245 2214 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.61 % Allowed : 17.36 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.19), residues: 1951 helix: 1.75 (0.23), residues: 538 sheet: 0.75 (0.20), residues: 634 loop : -0.02 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 363 TYR 0.024 0.001 TYR F 145 PHE 0.024 0.001 PHE J 432 TRP 0.033 0.001 TRP J 531 HIS 0.004 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00358 (15952) covalent geometry : angle 0.60731 (21652) SS BOND : bond 0.00409 ( 10) SS BOND : angle 0.80444 ( 20) hydrogen bonds : bond 0.03438 ( 762) hydrogen bonds : angle 4.90308 ( 2192) link_ALPHA1-4 : bond 0.00401 ( 2) link_ALPHA1-4 : angle 1.82768 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 196 time to evaluate : 0.605 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: C 59 ARG cc_start: 0.8579 (mmm-85) cc_final: 0.8337 (mmm-85) REVERT: E 1 ASP cc_start: 0.8584 (p0) cc_final: 0.8312 (p0) REVERT: E 154 ASP cc_start: 0.8662 (m-30) cc_final: 0.8353 (m-30) REVERT: F 17 GLU cc_start: 0.8440 (pm20) cc_final: 0.8232 (pm20) REVERT: F 166 GLU cc_start: 0.8520 (tt0) cc_final: 0.7966 (pp20) REVERT: H 166 GLU cc_start: 0.8554 (pm20) cc_final: 0.8325 (pm20) REVERT: H 175 ASP cc_start: 0.8001 (t0) cc_final: 0.7699 (t0) REVERT: I 43 LYS cc_start: 0.4494 (OUTLIER) cc_final: 0.2844 (mmmt) REVERT: I 70 PHE cc_start: 0.8655 (m-80) cc_final: 0.8112 (m-80) REVERT: I 157 MET cc_start: 0.8704 (ppp) cc_final: 0.8471 (ppp) REVERT: I 438 MET cc_start: 0.8812 (mmt) cc_final: 0.8380 (tpp) REVERT: I 446 ARG cc_start: 0.9025 (mtp180) cc_final: 0.8765 (mtm-85) REVERT: J 443 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7754 (tm-30) REVERT: J 459 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.7680 (mp-120) REVERT: J 466 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7523 (tm-30) outliers start: 44 outliers final: 23 residues processed: 228 average time/residue: 0.1277 time to fit residues: 42.2542 Evaluate side-chains 209 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 139 CYS Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 542 VAL Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 459 GLN Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 466 GLU Chi-restraints excluded: chain J residue 499 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 103 optimal weight: 8.9990 chunk 178 optimal weight: 30.0000 chunk 187 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 chunk 54 optimal weight: 0.4980 chunk 168 optimal weight: 2.9990 chunk 92 optimal weight: 0.0170 chunk 171 optimal weight: 4.9990 chunk 6 optimal weight: 0.0870 chunk 129 optimal weight: 2.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 GLN I 474 GLN J 182 ASN J 250 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.114807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.065873 restraints weight = 105030.999| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 5.24 r_work: 0.2844 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15964 Z= 0.132 Angle : 0.575 8.000 21678 Z= 0.290 Chirality : 0.041 0.156 2406 Planarity : 0.004 0.038 2776 Dihedral : 4.730 38.369 2211 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.96 % Allowed : 17.06 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.19), residues: 1951 helix: 1.89 (0.23), residues: 539 sheet: 0.74 (0.20), residues: 634 loop : -0.00 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 59 TYR 0.017 0.001 TYR F 145 PHE 0.021 0.001 PHE J 432 TRP 0.016 0.001 TRP J 167 HIS 0.004 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00307 (15952) covalent geometry : angle 0.57395 (21652) SS BOND : bond 0.00330 ( 10) SS BOND : angle 0.73043 ( 20) hydrogen bonds : bond 0.03162 ( 762) hydrogen bonds : angle 4.72571 ( 2192) link_ALPHA1-4 : bond 0.00673 ( 2) link_ALPHA1-4 : angle 1.41798 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 185 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ARG cc_start: 0.8553 (mmm-85) cc_final: 0.8284 (mmm-85) REVERT: C 81 LYS cc_start: 0.7936 (mttt) cc_final: 0.7517 (mttp) REVERT: D 69 GLN cc_start: 0.8796 (tt0) cc_final: 0.8478 (tp40) REVERT: D 106 ARG cc_start: 0.6877 (mmt90) cc_final: 0.6566 (mmm160) REVERT: E 1 ASP cc_start: 0.8638 (p0) cc_final: 0.8424 (p0) REVERT: E 103 ASP cc_start: 0.9255 (p0) cc_final: 0.9052 (p0) REVERT: E 154 ASP cc_start: 0.8658 (m-30) cc_final: 0.8338 (m-30) REVERT: F 17 GLU cc_start: 0.8447 (pm20) cc_final: 0.8195 (pm20) REVERT: F 166 GLU cc_start: 0.8520 (tt0) cc_final: 0.8022 (pp20) REVERT: G 73 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8027 (t0) REVERT: H 166 GLU cc_start: 0.8512 (pm20) cc_final: 0.8247 (pm20) REVERT: H 175 ASP cc_start: 0.8000 (t0) cc_final: 0.7618 (t0) REVERT: I 43 LYS cc_start: 0.4449 (OUTLIER) cc_final: 0.2745 (mmmt) REVERT: I 70 PHE cc_start: 0.8639 (m-80) cc_final: 0.8107 (m-80) REVERT: I 157 MET cc_start: 0.8628 (ppp) cc_final: 0.8343 (ppp) REVERT: I 446 ARG cc_start: 0.8986 (mtp180) cc_final: 0.8701 (mtm-85) REVERT: J 443 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7702 (tm-30) REVERT: J 459 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8159 (mp10) outliers start: 50 outliers final: 33 residues processed: 222 average time/residue: 0.1324 time to fit residues: 42.5058 Evaluate side-chains 218 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 131 HIS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 139 CYS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 378 MET Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 459 GLN Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain J residue 532 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 140 optimal weight: 0.9980 chunk 36 optimal weight: 0.0270 chunk 6 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 250 ASN J 459 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.114776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.075912 restraints weight = 156403.177| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 9.27 r_work: 0.2739 rms_B_bonded: 6.80 restraints_weight: 2.0000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15964 Z= 0.117 Angle : 0.551 6.884 21678 Z= 0.280 Chirality : 0.041 0.156 2406 Planarity : 0.004 0.047 2776 Dihedral : 4.250 38.907 2211 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.14 % Allowed : 16.65 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.19), residues: 1951 helix: 2.00 (0.23), residues: 541 sheet: 0.81 (0.20), residues: 624 loop : 0.03 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 59 TYR 0.019 0.001 TYR E 155 PHE 0.015 0.001 PHE J 432 TRP 0.010 0.001 TRP J 167 HIS 0.004 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00274 (15952) covalent geometry : angle 0.55059 (21652) SS BOND : bond 0.00317 ( 10) SS BOND : angle 0.71946 ( 20) hydrogen bonds : bond 0.02907 ( 762) hydrogen bonds : angle 4.56953 ( 2192) link_ALPHA1-4 : bond 0.00448 ( 2) link_ALPHA1-4 : angle 1.65289 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 192 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ARG cc_start: 0.8668 (mmm-85) cc_final: 0.8398 (mmm-85) REVERT: C 81 LYS cc_start: 0.8032 (mttt) cc_final: 0.7559 (mttp) REVERT: D 69 GLN cc_start: 0.8924 (tt0) cc_final: 0.8656 (tp40) REVERT: E 1 ASP cc_start: 0.8720 (p0) cc_final: 0.8372 (p0) REVERT: E 154 ASP cc_start: 0.8764 (m-30) cc_final: 0.8374 (m-30) REVERT: F 17 GLU cc_start: 0.8662 (pm20) cc_final: 0.8368 (pm20) REVERT: F 110 GLU cc_start: 0.9006 (tp30) cc_final: 0.8672 (tp30) REVERT: F 166 GLU cc_start: 0.8588 (tt0) cc_final: 0.8077 (pp20) REVERT: G 73 ASP cc_start: 0.8928 (OUTLIER) cc_final: 0.8334 (t0) REVERT: G 207 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.6719 (t0) REVERT: G 216 LYS cc_start: 0.8452 (tppt) cc_final: 0.7538 (tppt) REVERT: H 166 GLU cc_start: 0.8699 (pm20) cc_final: 0.8468 (pm20) REVERT: H 175 ASP cc_start: 0.8159 (t0) cc_final: 0.7809 (t0) REVERT: I 43 LYS cc_start: 0.4487 (OUTLIER) cc_final: 0.2748 (mmmt) REVERT: I 70 PHE cc_start: 0.8656 (m-80) cc_final: 0.8181 (m-80) REVERT: I 157 MET cc_start: 0.8722 (ppp) cc_final: 0.8389 (ppp) REVERT: I 446 ARG cc_start: 0.9139 (mtp180) cc_final: 0.8876 (mtm-85) REVERT: J 162 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8021 (tp30) REVERT: J 459 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.7537 (mp-120) outliers start: 53 outliers final: 35 residues processed: 231 average time/residue: 0.1220 time to fit residues: 41.3499 Evaluate side-chains 222 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 131 HIS Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 378 MET Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 453 LEU Chi-restraints excluded: chain J residue 459 GLN Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain J residue 542 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 53 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 459 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.110515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.070842 restraints weight = 136815.129| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 7.83 r_work: 0.2672 rms_B_bonded: 6.20 restraints_weight: 2.0000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 15964 Z= 0.278 Angle : 0.636 8.024 21678 Z= 0.326 Chirality : 0.043 0.182 2406 Planarity : 0.004 0.041 2776 Dihedral : 4.435 23.427 2211 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.61 % Allowed : 17.00 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.19), residues: 1951 helix: 1.94 (0.23), residues: 543 sheet: 0.70 (0.20), residues: 635 loop : 0.00 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 59 TYR 0.021 0.002 TYR F 145 PHE 0.026 0.002 PHE G 156 TRP 0.019 0.002 TRP J 167 HIS 0.007 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00642 (15952) covalent geometry : angle 0.63477 (21652) SS BOND : bond 0.00435 ( 10) SS BOND : angle 1.05063 ( 20) hydrogen bonds : bond 0.03345 ( 762) hydrogen bonds : angle 4.85195 ( 2192) link_ALPHA1-4 : bond 0.00490 ( 2) link_ALPHA1-4 : angle 1.81902 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 179 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 MET cc_start: 0.8579 (mtm) cc_final: 0.8355 (mtp) REVERT: D 69 GLN cc_start: 0.9026 (tt0) cc_final: 0.8805 (tp40) REVERT: E 1 ASP cc_start: 0.8923 (p0) cc_final: 0.8682 (p0) REVERT: E 154 ASP cc_start: 0.8809 (m-30) cc_final: 0.8400 (m-30) REVERT: F 69 THR cc_start: 0.9500 (OUTLIER) cc_final: 0.9241 (p) REVERT: F 110 GLU cc_start: 0.8995 (tp30) cc_final: 0.8669 (tp30) REVERT: F 166 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8025 (pp20) REVERT: G 73 ASP cc_start: 0.8958 (t0) cc_final: 0.8411 (t0) REVERT: H 148 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7881 (tm-30) REVERT: H 166 GLU cc_start: 0.8673 (pm20) cc_final: 0.8434 (pm20) REVERT: H 175 ASP cc_start: 0.8267 (t0) cc_final: 0.7880 (t0) REVERT: I 43 LYS cc_start: 0.4516 (OUTLIER) cc_final: 0.3774 (tptt) REVERT: I 70 PHE cc_start: 0.8691 (m-80) cc_final: 0.8171 (m-80) REVERT: I 157 MET cc_start: 0.8758 (ppp) cc_final: 0.8296 (ppp) REVERT: I 446 ARG cc_start: 0.9147 (mtp180) cc_final: 0.8866 (mtm-85) REVERT: I 489 THR cc_start: 0.8902 (m) cc_final: 0.8651 (p) outliers start: 61 outliers final: 41 residues processed: 228 average time/residue: 0.1134 time to fit residues: 37.9330 Evaluate side-chains 209 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 131 HIS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 166 GLU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 378 MET Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 453 LEU Chi-restraints excluded: chain J residue 459 GLN Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain J residue 532 THR Chi-restraints excluded: chain J residue 542 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 178 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 GLN J 250 ASN J 334 GLN ** J 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.111220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.070544 restraints weight = 131038.605| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 8.01 r_work: 0.2671 rms_B_bonded: 6.17 restraints_weight: 2.0000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 15964 Z= 0.247 Angle : 0.622 7.986 21678 Z= 0.317 Chirality : 0.043 0.175 2406 Planarity : 0.004 0.041 2776 Dihedral : 4.433 26.773 2211 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.73 % Allowed : 17.65 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.19), residues: 1951 helix: 1.92 (0.23), residues: 543 sheet: 0.65 (0.20), residues: 610 loop : 0.02 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 59 TYR 0.019 0.001 TYR F 145 PHE 0.023 0.001 PHE E 156 TRP 0.016 0.001 TRP E 47 HIS 0.007 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00576 (15952) covalent geometry : angle 0.62118 (21652) SS BOND : bond 0.00409 ( 10) SS BOND : angle 0.98864 ( 20) hydrogen bonds : bond 0.03212 ( 762) hydrogen bonds : angle 4.81147 ( 2192) link_ALPHA1-4 : bond 0.00472 ( 2) link_ALPHA1-4 : angle 1.76351 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 172 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ARG cc_start: 0.8650 (mmm-85) cc_final: 0.8341 (mmm-85) REVERT: C 129 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9183 (tttm) REVERT: D 69 GLN cc_start: 0.8997 (tt0) cc_final: 0.8754 (tp40) REVERT: E 1 ASP cc_start: 0.8895 (p0) cc_final: 0.8683 (p0) REVERT: E 151 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8191 (pt) REVERT: E 154 ASP cc_start: 0.8766 (m-30) cc_final: 0.8407 (m-30) REVERT: F 69 THR cc_start: 0.9455 (OUTLIER) cc_final: 0.9166 (p) REVERT: F 166 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8059 (pp20) REVERT: G 73 ASP cc_start: 0.8933 (t0) cc_final: 0.8335 (t0) REVERT: H 148 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7639 (tm-30) REVERT: H 166 GLU cc_start: 0.8645 (pm20) cc_final: 0.8386 (pm20) REVERT: H 175 ASP cc_start: 0.8242 (t0) cc_final: 0.7812 (t0) REVERT: I 43 LYS cc_start: 0.4422 (OUTLIER) cc_final: 0.3528 (tptt) REVERT: I 70 PHE cc_start: 0.8754 (m-80) cc_final: 0.8214 (m-80) REVERT: I 157 MET cc_start: 0.8682 (ppp) cc_final: 0.8181 (ppp) REVERT: I 294 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8045 (tp) REVERT: I 338 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9079 (tp) REVERT: I 446 ARG cc_start: 0.9105 (mtp180) cc_final: 0.8803 (mtm-85) REVERT: I 489 THR cc_start: 0.8844 (m) cc_final: 0.8607 (p) REVERT: J 459 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8061 (mp10) outliers start: 63 outliers final: 45 residues processed: 223 average time/residue: 0.1207 time to fit residues: 39.4619 Evaluate side-chains 219 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 166 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 131 HIS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 139 CYS Chi-restraints excluded: chain F residue 166 GLU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 365 THR Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 378 MET Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 453 LEU Chi-restraints excluded: chain J residue 459 GLN Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 473 SER Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain J residue 532 THR Chi-restraints excluded: chain J residue 542 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 195 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.111984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.063481 restraints weight = 130301.444| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 6.21 r_work: 0.2737 rms_B_bonded: 5.15 restraints_weight: 2.0000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15964 Z= 0.167 Angle : 0.592 7.420 21678 Z= 0.300 Chirality : 0.042 0.178 2406 Planarity : 0.004 0.045 2776 Dihedral : 4.333 28.865 2211 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.38 % Allowed : 18.31 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.19), residues: 1951 helix: 1.94 (0.23), residues: 544 sheet: 0.68 (0.20), residues: 634 loop : 0.02 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 59 TYR 0.017 0.001 TYR F 145 PHE 0.017 0.001 PHE E 156 TRP 0.014 0.001 TRP E 47 HIS 0.007 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00394 (15952) covalent geometry : angle 0.59124 (21652) SS BOND : bond 0.00340 ( 10) SS BOND : angle 0.84659 ( 20) hydrogen bonds : bond 0.03000 ( 762) hydrogen bonds : angle 4.70583 ( 2192) link_ALPHA1-4 : bond 0.00244 ( 2) link_ALPHA1-4 : angle 1.65382 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 175 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ARG cc_start: 0.8611 (mmm-85) cc_final: 0.8322 (mmm160) REVERT: C 129 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.9185 (tttm) REVERT: D 69 GLN cc_start: 0.8886 (tt0) cc_final: 0.8580 (tp40) REVERT: E 151 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8063 (pt) REVERT: E 154 ASP cc_start: 0.8683 (m-30) cc_final: 0.8347 (m-30) REVERT: F 69 THR cc_start: 0.9351 (OUTLIER) cc_final: 0.9039 (p) REVERT: F 110 GLU cc_start: 0.8920 (tp30) cc_final: 0.8694 (tp30) REVERT: F 166 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8084 (pp20) REVERT: F 192 GLU cc_start: 0.7468 (mp0) cc_final: 0.7255 (mp0) REVERT: G 73 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8166 (t0) REVERT: H 148 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7488 (tm-30) REVERT: H 166 GLU cc_start: 0.8600 (pm20) cc_final: 0.8329 (pm20) REVERT: H 175 ASP cc_start: 0.8122 (t0) cc_final: 0.7715 (t0) REVERT: I 43 LYS cc_start: 0.4479 (OUTLIER) cc_final: 0.4110 (tptt) REVERT: I 70 PHE cc_start: 0.8750 (m-80) cc_final: 0.8205 (m-80) REVERT: I 157 MET cc_start: 0.8599 (ppp) cc_final: 0.8046 (ppp) REVERT: I 338 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.9047 (tp) REVERT: I 438 MET cc_start: 0.8770 (mmt) cc_final: 0.8497 (tpp) REVERT: I 446 ARG cc_start: 0.9026 (mtp180) cc_final: 0.8719 (mtm-85) REVERT: I 489 THR cc_start: 0.8792 (m) cc_final: 0.8554 (p) outliers start: 57 outliers final: 42 residues processed: 219 average time/residue: 0.1237 time to fit residues: 40.0732 Evaluate side-chains 216 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 131 HIS Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 166 GLU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 378 MET Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 453 LEU Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 473 SER Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain J residue 532 THR Chi-restraints excluded: chain J residue 542 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 87 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 165 optimal weight: 0.0770 chunk 94 optimal weight: 0.5980 chunk 6 optimal weight: 0.1980 chunk 129 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 overall best weight: 1.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 459 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.111867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.064356 restraints weight = 136491.640| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 6.58 r_work: 0.2730 rms_B_bonded: 5.33 restraints_weight: 2.0000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15964 Z= 0.165 Angle : 0.595 7.533 21678 Z= 0.301 Chirality : 0.042 0.200 2406 Planarity : 0.004 0.045 2776 Dihedral : 4.301 29.735 2211 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.38 % Allowed : 18.48 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.19), residues: 1951 helix: 1.95 (0.23), residues: 544 sheet: 0.69 (0.20), residues: 633 loop : 0.02 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 59 TYR 0.016 0.001 TYR F 145 PHE 0.017 0.001 PHE E 156 TRP 0.013 0.001 TRP E 47 HIS 0.009 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00389 (15952) covalent geometry : angle 0.59445 (21652) SS BOND : bond 0.00350 ( 10) SS BOND : angle 0.84520 ( 20) hydrogen bonds : bond 0.02968 ( 762) hydrogen bonds : angle 4.68319 ( 2192) link_ALPHA1-4 : bond 0.00238 ( 2) link_ALPHA1-4 : angle 1.60647 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 169 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ARG cc_start: 0.8658 (mmm-85) cc_final: 0.8363 (mmm160) REVERT: C 126 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8127 (mt-10) REVERT: C 129 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.9159 (tttm) REVERT: D 69 GLN cc_start: 0.8892 (tt0) cc_final: 0.8649 (tp40) REVERT: D 82 MET cc_start: 0.6335 (ttt) cc_final: 0.6052 (ttp) REVERT: E 1 ASP cc_start: 0.8581 (p0) cc_final: 0.8325 (p0) REVERT: E 151 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8053 (pt) REVERT: E 154 ASP cc_start: 0.8710 (m-30) cc_final: 0.8391 (m-30) REVERT: F 69 THR cc_start: 0.9382 (OUTLIER) cc_final: 0.9076 (p) REVERT: F 110 GLU cc_start: 0.8958 (tp30) cc_final: 0.8694 (tp30) REVERT: F 166 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8060 (pp20) REVERT: F 190 ASP cc_start: 0.8124 (m-30) cc_final: 0.7852 (m-30) REVERT: F 192 GLU cc_start: 0.7490 (mp0) cc_final: 0.7268 (mp0) REVERT: G 73 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8196 (t0) REVERT: G 181 GLN cc_start: 0.7809 (pm20) cc_final: 0.7608 (pm20) REVERT: H 148 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7707 (tm-30) REVERT: H 166 GLU cc_start: 0.8591 (pm20) cc_final: 0.8324 (pm20) REVERT: H 175 ASP cc_start: 0.8163 (t0) cc_final: 0.7760 (t0) REVERT: I 43 LYS cc_start: 0.4445 (OUTLIER) cc_final: 0.4072 (tptt) REVERT: I 70 PHE cc_start: 0.8751 (m-80) cc_final: 0.8209 (m-80) REVERT: I 157 MET cc_start: 0.8566 (ppp) cc_final: 0.8029 (ppp) REVERT: I 294 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7998 (tp) REVERT: I 338 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9053 (tp) REVERT: I 438 MET cc_start: 0.8762 (mmt) cc_final: 0.8483 (tpp) REVERT: I 446 ARG cc_start: 0.9041 (mtp180) cc_final: 0.8733 (mtm-85) REVERT: I 489 THR cc_start: 0.8720 (m) cc_final: 0.8476 (p) REVERT: J 169 LEU cc_start: 0.9275 (mp) cc_final: 0.9071 (tp) outliers start: 57 outliers final: 40 residues processed: 213 average time/residue: 0.1326 time to fit residues: 41.6333 Evaluate side-chains 214 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 131 HIS Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 139 CYS Chi-restraints excluded: chain F residue 166 GLU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 365 THR Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 453 LEU Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 473 SER Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain J residue 532 THR Chi-restraints excluded: chain J residue 542 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 103 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 175 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 95 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.112483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.065238 restraints weight = 132857.634| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 6.62 r_work: 0.2748 rms_B_bonded: 5.33 restraints_weight: 2.0000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15964 Z= 0.131 Angle : 0.599 8.675 21678 Z= 0.300 Chirality : 0.042 0.177 2406 Planarity : 0.004 0.050 2776 Dihedral : 4.245 30.831 2211 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.26 % Allowed : 18.78 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.19), residues: 1951 helix: 1.98 (0.23), residues: 543 sheet: 0.72 (0.20), residues: 623 loop : 0.00 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 59 TYR 0.015 0.001 TYR I 521 PHE 0.014 0.001 PHE E 156 TRP 0.014 0.001 TRP J 103 HIS 0.008 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00311 (15952) covalent geometry : angle 0.59860 (21652) SS BOND : bond 0.00323 ( 10) SS BOND : angle 0.73751 ( 20) hydrogen bonds : bond 0.02844 ( 762) hydrogen bonds : angle 4.59859 ( 2192) link_ALPHA1-4 : bond 0.00261 ( 2) link_ALPHA1-4 : angle 1.47212 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 173 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 ARG cc_start: 0.8623 (mmm-85) cc_final: 0.8323 (mmm160) REVERT: C 129 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.8968 (tptm) REVERT: D 69 GLN cc_start: 0.8865 (tt0) cc_final: 0.8596 (tp40) REVERT: D 82 MET cc_start: 0.6447 (ttt) cc_final: 0.6172 (ttp) REVERT: D 116 GLN cc_start: 0.8771 (mp10) cc_final: 0.8509 (mp10) REVERT: E 1 ASP cc_start: 0.8514 (p0) cc_final: 0.8272 (p0) REVERT: E 151 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8049 (pt) REVERT: E 153 LYS cc_start: 0.7985 (tptt) cc_final: 0.7713 (tttt) REVERT: E 154 ASP cc_start: 0.8752 (m-30) cc_final: 0.8438 (m-30) REVERT: F 17 GLU cc_start: 0.8689 (pm20) cc_final: 0.8234 (pm20) REVERT: F 69 THR cc_start: 0.9369 (OUTLIER) cc_final: 0.9057 (p) REVERT: F 110 GLU cc_start: 0.8990 (tp30) cc_final: 0.8725 (tp30) REVERT: F 166 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8092 (pp20) REVERT: F 190 ASP cc_start: 0.8155 (m-30) cc_final: 0.7859 (m-30) REVERT: F 192 GLU cc_start: 0.7488 (mp0) cc_final: 0.7286 (mp0) REVERT: G 73 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8179 (t0) REVERT: G 181 GLN cc_start: 0.7824 (pm20) cc_final: 0.7614 (pm20) REVERT: H 148 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7565 (tm-30) REVERT: H 166 GLU cc_start: 0.8595 (pm20) cc_final: 0.8336 (pm20) REVERT: H 175 ASP cc_start: 0.8160 (t0) cc_final: 0.7747 (t0) REVERT: I 43 LYS cc_start: 0.4456 (OUTLIER) cc_final: 0.4097 (tptt) REVERT: I 70 PHE cc_start: 0.8722 (m-80) cc_final: 0.8156 (m-80) REVERT: I 157 MET cc_start: 0.8560 (ppp) cc_final: 0.8017 (ppp) REVERT: I 338 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.9055 (tp) REVERT: I 438 MET cc_start: 0.8739 (mmt) cc_final: 0.8461 (tpp) REVERT: I 446 ARG cc_start: 0.9037 (mtp180) cc_final: 0.8720 (mtm-85) REVERT: I 489 THR cc_start: 0.8714 (m) cc_final: 0.8465 (p) outliers start: 55 outliers final: 42 residues processed: 216 average time/residue: 0.1290 time to fit residues: 41.3610 Evaluate side-chains 219 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 131 HIS Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 139 CYS Chi-restraints excluded: chain F residue 166 GLU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 365 THR Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 453 LEU Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 473 SER Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain J residue 532 THR Chi-restraints excluded: chain J residue 542 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 49 optimal weight: 3.9990 chunk 82 optimal weight: 30.0000 chunk 159 optimal weight: 10.0000 chunk 156 optimal weight: 20.0000 chunk 135 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.111771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.071870 restraints weight = 142814.315| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 8.26 r_work: 0.2693 rms_B_bonded: 6.37 restraints_weight: 2.0000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15964 Z= 0.172 Angle : 0.619 9.664 21678 Z= 0.311 Chirality : 0.042 0.181 2406 Planarity : 0.004 0.049 2776 Dihedral : 4.272 30.761 2211 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.02 % Allowed : 18.84 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.19), residues: 1951 helix: 1.99 (0.23), residues: 543 sheet: 0.70 (0.20), residues: 633 loop : 0.03 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 59 TYR 0.016 0.001 TYR F 145 PHE 0.017 0.001 PHE E 156 TRP 0.015 0.001 TRP J 103 HIS 0.008 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00407 (15952) covalent geometry : angle 0.61798 (21652) SS BOND : bond 0.00345 ( 10) SS BOND : angle 0.85546 ( 20) hydrogen bonds : bond 0.02917 ( 762) hydrogen bonds : angle 4.64623 ( 2192) link_ALPHA1-4 : bond 0.00256 ( 2) link_ALPHA1-4 : angle 1.47815 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 0.393 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: C 59 ARG cc_start: 0.8702 (mmm-85) cc_final: 0.8378 (mmm-85) REVERT: C 129 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.8993 (tptm) REVERT: D 82 MET cc_start: 0.6556 (ttt) cc_final: 0.6284 (ttp) REVERT: D 116 GLN cc_start: 0.8777 (mp10) cc_final: 0.8546 (mp10) REVERT: E 1 ASP cc_start: 0.8630 (p0) cc_final: 0.8262 (p0) REVERT: E 151 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8133 (pt) REVERT: E 153 LYS cc_start: 0.8100 (tptt) cc_final: 0.7814 (tttt) REVERT: E 154 ASP cc_start: 0.8801 (m-30) cc_final: 0.8466 (m-30) REVERT: F 69 THR cc_start: 0.9461 (OUTLIER) cc_final: 0.9177 (p) REVERT: F 110 GLU cc_start: 0.9085 (tp30) cc_final: 0.8829 (tp30) REVERT: F 166 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8091 (pp20) REVERT: F 190 ASP cc_start: 0.8228 (m-30) cc_final: 0.7984 (m-30) REVERT: G 73 ASP cc_start: 0.8949 (t0) cc_final: 0.8357 (t0) REVERT: G 181 GLN cc_start: 0.8036 (pm20) cc_final: 0.7832 (pm20) REVERT: H 148 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7777 (tm-30) REVERT: H 166 GLU cc_start: 0.8657 (pm20) cc_final: 0.8405 (pm20) REVERT: H 175 ASP cc_start: 0.8292 (t0) cc_final: 0.7888 (t0) REVERT: H 191 TYR cc_start: 0.8218 (t80) cc_final: 0.8005 (t80) REVERT: I 43 LYS cc_start: 0.4404 (OUTLIER) cc_final: 0.4023 (tptt) REVERT: I 70 PHE cc_start: 0.8796 (m-80) cc_final: 0.8202 (m-80) REVERT: I 157 MET cc_start: 0.8655 (ppp) cc_final: 0.8108 (ppp) REVERT: I 294 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8043 (tp) REVERT: I 338 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.9076 (tp) REVERT: I 438 MET cc_start: 0.8781 (mmt) cc_final: 0.8509 (tpp) REVERT: I 446 ARG cc_start: 0.9139 (mtp180) cc_final: 0.8838 (mtm-85) REVERT: I 489 THR cc_start: 0.8765 (m) cc_final: 0.8509 (p) REVERT: J 169 LEU cc_start: 0.9259 (mp) cc_final: 0.9021 (tp) outliers start: 51 outliers final: 43 residues processed: 211 average time/residue: 0.1099 time to fit residues: 34.1718 Evaluate side-chains 220 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 131 HIS Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 94 CYS Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 139 CYS Chi-restraints excluded: chain F residue 166 GLU Chi-restraints excluded: chain F residue 168 VAL Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 43 MET Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 93 MET Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain H residue 23 CYS Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 113 ILE Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 294 LEU Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 365 THR Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain J residue 166 THR Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 453 LEU Chi-restraints excluded: chain J residue 461 THR Chi-restraints excluded: chain J residue 473 SER Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain J residue 532 THR Chi-restraints excluded: chain J residue 542 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 120 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 186 optimal weight: 0.9990 chunk 175 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 177 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 212 HIS J 447 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.111862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.072290 restraints weight = 143113.678| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 8.60 r_work: 0.2687 rms_B_bonded: 6.47 restraints_weight: 2.0000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15964 Z= 0.168 Angle : 0.625 9.867 21678 Z= 0.314 Chirality : 0.042 0.193 2406 Planarity : 0.004 0.050 2776 Dihedral : 4.294 31.486 2211 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.14 % Allowed : 19.14 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.19), residues: 1951 helix: 1.99 (0.22), residues: 543 sheet: 0.70 (0.20), residues: 623 loop : 0.02 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 59 TYR 0.015 0.001 TYR F 145 PHE 0.017 0.001 PHE E 156 TRP 0.014 0.001 TRP J 103 HIS 0.008 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00399 (15952) covalent geometry : angle 0.62399 (21652) SS BOND : bond 0.00343 ( 10) SS BOND : angle 0.82541 ( 20) hydrogen bonds : bond 0.02891 ( 762) hydrogen bonds : angle 4.64002 ( 2192) link_ALPHA1-4 : bond 0.00305 ( 2) link_ALPHA1-4 : angle 1.43549 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5413.57 seconds wall clock time: 93 minutes 4.92 seconds (5584.92 seconds total)