Starting phenix.real_space_refine on Thu Feb 15 03:52:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rbt_24401/02_2024/7rbt_24401_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rbt_24401/02_2024/7rbt_24401.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rbt_24401/02_2024/7rbt_24401_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rbt_24401/02_2024/7rbt_24401_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rbt_24401/02_2024/7rbt_24401_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rbt_24401/02_2024/7rbt_24401.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rbt_24401/02_2024/7rbt_24401.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rbt_24401/02_2024/7rbt_24401_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rbt_24401/02_2024/7rbt_24401_neut_updated.pdb" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 63 5.16 5 C 6915 2.51 5 N 1903 2.21 5 O 1999 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "P GLU 3": "OE1" <-> "OE2" Residue "R GLU 48": "OE1" <-> "OE2" Residue "R GLU 119": "OE1" <-> "OE2" Residue "R ARG 136": "NH1" <-> "NH2" Residue "R ARG 163": "NH1" <-> "NH2" Residue "R ARG 164": "NH1" <-> "NH2" Residue "R ARG 169": "NH1" <-> "NH2" Residue "R ARG 190": "NH1" <-> "NH2" Residue "R ARG 192": "NH1" <-> "NH2" Residue "R ARG 257": "NH1" <-> "NH2" Residue "R GLU 282": "OE1" <-> "OE2" Residue "R GLU 291": "OE1" <-> "OE2" Residue "R ARG 300": "NH1" <-> "NH2" Residue "R ARG 326": "NH1" <-> "NH2" Residue "R ARG 328": "NH1" <-> "NH2" Residue "R ARG 336": "NH1" <-> "NH2" Residue "R ARG 338": "NH1" <-> "NH2" Residue "R ARG 341": "NH1" <-> "NH2" Residue "R GLU 354": "OE1" <-> "OE2" Residue "R GLU 377": "OE1" <-> "OE2" Residue "R ARG 405": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10881 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1792 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2581 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 969 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "P" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 246 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3109 Unusual residues: {'41Y': 1} Classifications: {'peptide': 378, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 363, None: 1} Not linked: pdbres="ARG R 411 " pdbres="41Y R 501 " Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 5.76, per 1000 atoms: 0.53 Number of scatterers: 10881 At special positions: 0 Unit cell: (167.232, 124.8, 104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 F 1 9.00 O 1999 8.00 N 1903 7.00 C 6915 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 70 " distance=2.04 Simple disulfide: pdb=" SG CYS R 61 " - pdb=" SG CYS R 103 " distance=2.03 Simple disulfide: pdb=" SG CYS R 84 " - pdb=" SG CYS R 118 " distance=2.03 Simple disulfide: pdb=" SG CYS R 216 " - pdb=" SG CYS R 286 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.52 Conformation dependent library (CDL) restraints added in 2.0 seconds 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2570 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 18 sheets defined 30.4% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.882A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 332 through 351 Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 42 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'P' and resid 4 through 28 Processing helix chain 'R' and resid 32 through 52 Processing helix chain 'R' and resid 127 through 160 Processing helix chain 'R' and resid 168 through 192 Processing helix chain 'R' and resid 210 through 246 Processing helix chain 'R' and resid 253 through 265 Processing helix chain 'R' and resid 267 through 280 Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 294 through 326 removed outlier: 4.811A pdb=" N ILE R 299 " --> pdb=" O ILE R 295 " (cutoff:3.500A) Proline residue: R 302 - end of helix Processing helix chain 'R' and resid 337 through 347 Processing helix chain 'R' and resid 363 through 365 No H-bonds generated for 'chain 'R' and resid 363 through 365' Processing helix chain 'R' and resid 369 through 372 No H-bonds generated for 'chain 'R' and resid 369 through 372' Processing helix chain 'R' and resid 374 through 393 removed outlier: 5.379A pdb=" N GLY R 385 " --> pdb=" O SER R 381 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N PHE R 386 " --> pdb=" O SER R 382 " (cutoff:3.500A) Processing helix chain 'R' and resid 397 through 409 Processing sheet with id= A, first strand: chain 'A' and resid 243 through 245 removed outlier: 4.143A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.300A pdb=" N PHE A 290 " --> pdb=" O VAL A 248 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.633A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.972A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.622A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 146 through 149 removed outlier: 6.798A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.845A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.145A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 284 through 288 removed outlier: 3.512A pdb=" N VAL B 296 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.721A pdb=" N LEU E 20 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.489A pdb=" N THR E 118 " --> pdb=" O VAL E 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 92 through 99 removed outlier: 4.024A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.116A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 213 through 219 removed outlier: 3.714A pdb=" N VAL E 214 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.517A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'N' and resid 11 through 13 removed outlier: 6.266A pdb=" N THR N 125 " --> pdb=" O VAL N 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.728A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TRP N 36 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'R' and resid 78 through 80 removed outlier: 4.037A pdb=" N ALA R 78 " --> pdb=" O CYS R 103 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG R 101 " --> pdb=" O ALA R 80 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1233 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: 3.02 Time building geometry restraints manager: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3092 1.33 - 1.46: 2759 1.46 - 1.58: 5183 1.58 - 1.71: 3 1.71 - 1.83: 87 Bond restraints: 11124 Sorted by residual: bond pdb=" C24 41Y R 501 " pdb=" C25 41Y R 501 " ideal model delta sigma weight residual 1.586 1.384 0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C11 41Y R 501 " pdb=" N10 41Y R 501 " ideal model delta sigma weight residual 1.453 1.341 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" C08 41Y R 501 " pdb=" C09 41Y R 501 " ideal model delta sigma weight residual 1.501 1.593 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C09 41Y R 501 " pdb=" N10 41Y R 501 " ideal model delta sigma weight residual 1.489 1.398 0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C06 41Y R 501 " pdb=" C07 41Y R 501 " ideal model delta sigma weight residual 1.391 1.312 0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 11119 not shown) Histogram of bond angle deviations from ideal: 98.63 - 105.74: 176 105.74 - 112.84: 5838 112.84 - 119.95: 4006 119.95 - 127.06: 4928 127.06 - 134.16: 150 Bond angle restraints: 15098 Sorted by residual: angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 112.23 104.49 7.74 1.26e+00 6.30e-01 3.77e+01 angle pdb=" CA ASP B 76 " pdb=" CB ASP B 76 " pdb=" CG ASP B 76 " ideal model delta sigma weight residual 112.60 117.65 -5.05 1.00e+00 1.00e+00 2.55e+01 angle pdb=" N AIB P 2 " pdb=" CA AIB P 2 " pdb=" C AIB P 2 " ideal model delta sigma weight residual 111.00 120.49 -9.49 2.80e+00 1.28e-01 1.15e+01 angle pdb=" N ASP B 298 " pdb=" CA ASP B 298 " pdb=" C ASP B 298 " ideal model delta sigma weight residual 110.30 105.54 4.76 1.50e+00 4.44e-01 1.01e+01 angle pdb=" N VAL N 110 " pdb=" CA VAL N 110 " pdb=" C VAL N 110 " ideal model delta sigma weight residual 113.07 108.89 4.18 1.37e+00 5.33e-01 9.31e+00 ... (remaining 15093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 5873 17.58 - 35.16: 529 35.16 - 52.74: 112 52.74 - 70.32: 23 70.32 - 87.89: 13 Dihedral angle restraints: 6550 sinusoidal: 2551 harmonic: 3999 Sorted by residual: dihedral pdb=" CA THR E 160 " pdb=" C THR E 160 " pdb=" N TYR E 161 " pdb=" CA TYR E 161 " ideal model delta harmonic sigma weight residual 180.00 -155.37 -24.63 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA CYS R 167 " pdb=" C CYS R 167 " pdb=" N THR R 168 " pdb=" CA THR R 168 " ideal model delta harmonic sigma weight residual 180.00 156.58 23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA TRP B 63 " pdb=" C TRP B 63 " pdb=" N GLY B 64 " pdb=" CA GLY B 64 " ideal model delta harmonic sigma weight residual 180.00 160.21 19.79 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 6547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1068 0.038 - 0.077: 432 0.077 - 0.115: 135 0.115 - 0.153: 32 0.153 - 0.192: 6 Chirality restraints: 1673 Sorted by residual: chirality pdb=" C22 41Y R 501 " pdb=" C06 41Y R 501 " pdb=" C23 41Y R 501 " pdb=" N10 41Y R 501 " both_signs ideal model delta sigma weight residual False -2.70 -2.51 -0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CA ASP B 76 " pdb=" N ASP B 76 " pdb=" C ASP B 76 " pdb=" CB ASP B 76 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.14e-01 chirality pdb=" CA ASP B 298 " pdb=" N ASP B 298 " pdb=" C ASP B 298 " pdb=" CB ASP B 298 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 1670 not shown) Planarity restraints: 1921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY P 4 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.16e+00 pdb=" C GLY P 4 " -0.052 2.00e-02 2.50e+03 pdb=" O GLY P 4 " 0.020 2.00e-02 2.50e+03 pdb=" N THR P 5 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 371 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C PHE R 371 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE R 371 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA R 372 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 141 " -0.016 2.00e-02 2.50e+03 1.66e-02 5.51e+00 pdb=" CG TYR R 141 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR R 141 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR R 141 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR R 141 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR R 141 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR R 141 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR R 141 " 0.004 2.00e-02 2.50e+03 ... (remaining 1918 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 241 2.65 - 3.22: 11290 3.22 - 3.78: 16705 3.78 - 4.34: 24222 4.34 - 4.90: 38483 Nonbonded interactions: 90941 Sorted by model distance: nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.093 2.440 nonbonded pdb=" NH1 ARG R 190 " pdb=" OD1 ASP R 191 " model vdw 2.135 2.520 nonbonded pdb=" O THR B 274 " pdb=" OG SER B 275 " model vdw 2.137 2.440 nonbonded pdb=" NE2 GLN E 82 " pdb=" O MET E 83 " model vdw 2.155 2.520 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.218 2.440 ... (remaining 90936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.280 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 30.820 Find NCS groups from input model: 0.320 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 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 : 0.007 0.202 11124 Z= 0.464 Angle : 0.756 9.489 15098 Z= 0.419 Chirality : 0.046 0.192 1673 Planarity : 0.005 0.053 1921 Dihedral : 14.727 87.894 3956 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.70 % Allowed : 1.75 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.21), residues: 1353 helix: -0.63 (0.23), residues: 421 sheet: -2.34 (0.26), residues: 342 loop : -2.42 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP P 25 HIS 0.010 0.002 HIS R 166 PHE 0.030 0.002 PHE R 270 TYR 0.041 0.003 TYR R 141 ARG 0.018 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 195 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7048 (mtp-110) cc_final: 0.6483 (mtp85) REVERT: B 23 LYS cc_start: 0.7663 (ttpp) cc_final: 0.7374 (ttmt) REVERT: B 76 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7458 (p0) REVERT: R 109 TRP cc_start: 0.2406 (m100) cc_final: 0.2028 (m100) REVERT: R 199 PRO cc_start: 0.6800 (Cg_endo) cc_final: 0.6509 (Cg_exo) REVERT: R 204 GLN cc_start: 0.4612 (tp40) cc_final: 0.4350 (tp40) REVERT: R 287 TRP cc_start: 0.6442 (m-10) cc_final: 0.5939 (m-10) REVERT: R 395 ILE cc_start: 0.7583 (mm) cc_final: 0.7331 (mm) outliers start: 8 outliers final: 2 residues processed: 201 average time/residue: 0.2604 time to fit residues: 71.3877 Evaluate side-chains 167 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 164 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 HIS ** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11124 Z= 0.301 Angle : 0.737 11.333 15098 Z= 0.375 Chirality : 0.047 0.195 1673 Planarity : 0.005 0.049 1921 Dihedral : 6.187 59.536 1539 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.62 % Allowed : 9.61 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.22), residues: 1353 helix: 0.09 (0.24), residues: 415 sheet: -1.91 (0.28), residues: 313 loop : -1.94 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP P 25 HIS 0.007 0.001 HIS A 357 PHE 0.023 0.002 PHE R 270 TYR 0.029 0.002 TYR R 259 ARG 0.008 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7038 (mtp-110) cc_final: 0.6541 (mtp85) REVERT: B 23 LYS cc_start: 0.7641 (ttpp) cc_final: 0.7321 (ttmt) REVERT: B 211 TRP cc_start: 0.8019 (m100) cc_final: 0.7812 (m100) REVERT: E 148 ARG cc_start: 0.5990 (mmp80) cc_final: 0.5679 (mmt90) REVERT: E 215 TYR cc_start: 0.7478 (m-10) cc_final: 0.7273 (m-80) REVERT: R 37 GLN cc_start: 0.7203 (mm110) cc_final: 0.6232 (tm-30) REVERT: R 140 MET cc_start: 0.7337 (tmm) cc_final: 0.7107 (tmm) REVERT: R 199 PRO cc_start: 0.6587 (Cg_endo) cc_final: 0.6350 (Cg_exo) REVERT: R 287 TRP cc_start: 0.6300 (m-10) cc_final: 0.5279 (m-10) REVERT: R 395 ILE cc_start: 0.7636 (mm) cc_final: 0.7378 (mm) outliers start: 30 outliers final: 23 residues processed: 200 average time/residue: 0.2873 time to fit residues: 76.6554 Evaluate side-chains 176 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 115 HIS Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 407 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 122 optimal weight: 0.0670 chunk 132 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN E 82 GLN N 1 GLN N 3 GLN P 19 GLN ** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11124 Z= 0.166 Angle : 0.634 11.547 15098 Z= 0.318 Chirality : 0.043 0.198 1673 Planarity : 0.004 0.046 1921 Dihedral : 5.430 59.727 1537 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.41 % Allowed : 12.66 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.23), residues: 1353 helix: 0.78 (0.25), residues: 421 sheet: -1.41 (0.29), residues: 314 loop : -1.68 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 233 HIS 0.005 0.001 HIS R 166 PHE 0.017 0.001 PHE B 253 TYR 0.021 0.001 TYR R 141 ARG 0.005 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 199 time to evaluate : 1.434 Fit side-chains revert: symmetry clash REVERT: A 55 THR cc_start: 0.4326 (m) cc_final: 0.4048 (m) REVERT: A 342 ARG cc_start: 0.6678 (ttp80) cc_final: 0.6450 (ttt-90) REVERT: B 19 ARG cc_start: 0.7082 (mtp-110) cc_final: 0.6482 (mtp85) REVERT: B 23 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7395 (ttmt) REVERT: B 52 ARG cc_start: 0.7192 (ptp-110) cc_final: 0.6891 (mtt-85) REVERT: B 336 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7750 (mp) REVERT: E 215 TYR cc_start: 0.7331 (m-10) cc_final: 0.7110 (m-80) REVERT: G 46 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.6312 (mmtm) REVERT: R 37 GLN cc_start: 0.6995 (mm110) cc_final: 0.6295 (tm-30) REVERT: R 140 MET cc_start: 0.7384 (tmm) cc_final: 0.7117 (tmm) REVERT: R 165 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6840 (pp) REVERT: R 182 LEU cc_start: 0.6537 (tp) cc_final: 0.6157 (tp) REVERT: R 183 ARG cc_start: 0.6259 (OUTLIER) cc_final: 0.5632 (ttm170) REVERT: R 199 PRO cc_start: 0.6500 (Cg_endo) cc_final: 0.6242 (Cg_exo) REVERT: R 287 TRP cc_start: 0.6001 (m-10) cc_final: 0.4810 (m-10) REVERT: R 305 MET cc_start: 0.6541 (mmp) cc_final: 0.6089 (mmt) REVERT: R 395 ILE cc_start: 0.7628 (mm) cc_final: 0.7360 (mm) outliers start: 39 outliers final: 23 residues processed: 229 average time/residue: 0.2772 time to fit residues: 84.0864 Evaluate side-chains 194 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 203 ASP Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 407 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 63 optimal weight: 0.4980 chunk 13 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 82 optimal weight: 0.0030 chunk 123 optimal weight: 6.9990 chunk 130 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 1 GLN N 3 GLN P 19 GLN R 204 GLN ** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11124 Z= 0.157 Angle : 0.621 11.496 15098 Z= 0.307 Chirality : 0.043 0.281 1673 Planarity : 0.004 0.045 1921 Dihedral : 5.138 56.556 1537 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.58 % Allowed : 15.02 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.23), residues: 1353 helix: 0.94 (0.25), residues: 425 sheet: -1.33 (0.28), residues: 319 loop : -1.52 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 233 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE R 270 TYR 0.022 0.001 TYR R 141 ARG 0.006 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 189 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7148 (mtp-110) cc_final: 0.6564 (mtp85) REVERT: B 52 ARG cc_start: 0.7150 (ptp-110) cc_final: 0.6946 (mtt-85) REVERT: B 211 TRP cc_start: 0.7728 (m100) cc_final: 0.7466 (m100) REVERT: B 336 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7741 (mp) REVERT: G 46 LYS cc_start: 0.6687 (OUTLIER) cc_final: 0.6328 (mmtm) REVERT: R 39 TRP cc_start: 0.6792 (t60) cc_final: 0.6377 (t60) REVERT: R 109 TRP cc_start: 0.2373 (m100) cc_final: 0.1728 (m100) REVERT: R 165 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6864 (pp) REVERT: R 182 LEU cc_start: 0.6548 (tp) cc_final: 0.6254 (tp) REVERT: R 183 ARG cc_start: 0.6147 (OUTLIER) cc_final: 0.5202 (ttm170) REVERT: R 199 PRO cc_start: 0.6465 (Cg_endo) cc_final: 0.6207 (Cg_exo) REVERT: R 287 TRP cc_start: 0.5944 (m-10) cc_final: 0.4747 (m-10) REVERT: R 395 ILE cc_start: 0.7698 (mm) cc_final: 0.7410 (mm) outliers start: 41 outliers final: 26 residues processed: 216 average time/residue: 0.2786 time to fit residues: 80.7045 Evaluate side-chains 192 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 203 ASP Chi-restraints excluded: chain R residue 407 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 117 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 3 GLN P 19 GLN R 93 HIS R 117 GLN R 204 GLN ** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11124 Z= 0.224 Angle : 0.630 11.837 15098 Z= 0.317 Chirality : 0.044 0.315 1673 Planarity : 0.004 0.045 1921 Dihedral : 5.214 58.307 1536 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.67 % Allowed : 17.12 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.23), residues: 1353 helix: 0.92 (0.25), residues: 426 sheet: -1.37 (0.28), residues: 322 loop : -1.40 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 233 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE B 253 TYR 0.023 0.002 TYR R 259 ARG 0.005 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 169 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 ARG cc_start: 0.7265 (ptp-170) cc_final: 0.7007 (mtt-85) REVERT: B 211 TRP cc_start: 0.7794 (m100) cc_final: 0.7579 (m100) REVERT: B 336 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7774 (mp) REVERT: G 46 LYS cc_start: 0.6715 (OUTLIER) cc_final: 0.6395 (mmtm) REVERT: R 109 TRP cc_start: 0.2518 (m100) cc_final: 0.1832 (m100) REVERT: R 140 MET cc_start: 0.7433 (tmm) cc_final: 0.7148 (tmm) REVERT: R 165 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6786 (pp) REVERT: R 182 LEU cc_start: 0.6445 (tp) cc_final: 0.5990 (mp) REVERT: R 187 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7686 (tp) REVERT: R 199 PRO cc_start: 0.6401 (Cg_endo) cc_final: 0.6133 (Cg_exo) REVERT: R 203 ASP cc_start: 0.5015 (OUTLIER) cc_final: 0.4548 (p0) REVERT: R 252 GLU cc_start: 0.4280 (OUTLIER) cc_final: 0.3956 (pm20) REVERT: R 287 TRP cc_start: 0.5883 (m-10) cc_final: 0.4872 (m-10) REVERT: R 300 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.5737 (mtm110) REVERT: R 395 ILE cc_start: 0.7649 (mm) cc_final: 0.7378 (mm) outliers start: 42 outliers final: 28 residues processed: 204 average time/residue: 0.2826 time to fit residues: 77.1607 Evaluate side-chains 198 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 203 ASP Chi-restraints excluded: chain R residue 252 GLU Chi-restraints excluded: chain R residue 293 LYS Chi-restraints excluded: chain R residue 300 ARG Chi-restraints excluded: chain R residue 301 THR Chi-restraints excluded: chain R residue 407 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 108 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 68 optimal weight: 0.0050 chunk 125 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN N 1 GLN P 19 GLN R 93 HIS R 204 GLN ** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11124 Z= 0.154 Angle : 0.592 11.073 15098 Z= 0.295 Chirality : 0.042 0.173 1673 Planarity : 0.004 0.046 1921 Dihedral : 4.940 55.618 1536 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.02 % Allowed : 17.90 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.23), residues: 1353 helix: 1.05 (0.25), residues: 432 sheet: -1.13 (0.28), residues: 308 loop : -1.36 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 233 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.001 PHE B 253 TYR 0.022 0.001 TYR R 141 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 180 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 ASN cc_start: 0.6728 (OUTLIER) cc_final: 0.6341 (t0) REVERT: B 19 ARG cc_start: 0.7080 (mtp-110) cc_final: 0.6495 (mtp85) REVERT: B 52 ARG cc_start: 0.7185 (ptp-170) cc_final: 0.6929 (mtt-85) REVERT: B 211 TRP cc_start: 0.7695 (m100) cc_final: 0.7398 (m100) REVERT: B 336 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7773 (mp) REVERT: G 46 LYS cc_start: 0.6731 (OUTLIER) cc_final: 0.6310 (mmtm) REVERT: R 39 TRP cc_start: 0.6836 (t60) cc_final: 0.6405 (t60) REVERT: R 109 TRP cc_start: 0.2441 (m100) cc_final: 0.1811 (m100) REVERT: R 140 MET cc_start: 0.7386 (tmm) cc_final: 0.7121 (tmm) REVERT: R 165 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6776 (pp) REVERT: R 183 ARG cc_start: 0.6083 (OUTLIER) cc_final: 0.5503 (ttm170) REVERT: R 199 PRO cc_start: 0.6428 (Cg_endo) cc_final: 0.6175 (Cg_exo) REVERT: R 203 ASP cc_start: 0.5048 (OUTLIER) cc_final: 0.4575 (p0) REVERT: R 284 THR cc_start: 0.7764 (t) cc_final: 0.7544 (t) REVERT: R 287 TRP cc_start: 0.5886 (m-10) cc_final: 0.5202 (m-10) REVERT: R 300 ARG cc_start: 0.6157 (OUTLIER) cc_final: 0.5774 (mtm110) REVERT: R 305 MET cc_start: 0.6514 (mmp) cc_final: 0.6163 (mmt) REVERT: R 395 ILE cc_start: 0.7678 (mm) cc_final: 0.7371 (mm) outliers start: 46 outliers final: 26 residues processed: 215 average time/residue: 0.2873 time to fit residues: 82.3796 Evaluate side-chains 202 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 169 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 203 ASP Chi-restraints excluded: chain R residue 293 LYS Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain R residue 300 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 0.0020 chunk 109 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN P 19 GLN R 93 HIS R 204 GLN ** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11124 Z= 0.200 Angle : 0.618 11.303 15098 Z= 0.307 Chirality : 0.043 0.184 1673 Planarity : 0.004 0.046 1921 Dihedral : 4.975 56.550 1536 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.84 % Allowed : 18.17 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.23), residues: 1353 helix: 1.10 (0.25), residues: 428 sheet: -1.09 (0.28), residues: 308 loop : -1.30 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 233 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.001 PHE R 270 TYR 0.020 0.002 TYR R 141 ARG 0.007 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 167 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7054 (mtp-110) cc_final: 0.6528 (mtp85) REVERT: B 44 GLN cc_start: 0.6507 (OUTLIER) cc_final: 0.6098 (pm20) REVERT: B 211 TRP cc_start: 0.7723 (m100) cc_final: 0.7483 (m100) REVERT: B 336 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7753 (mp) REVERT: G 46 LYS cc_start: 0.6804 (OUTLIER) cc_final: 0.6335 (mmtm) REVERT: R 39 TRP cc_start: 0.6831 (t60) cc_final: 0.6386 (t60) REVERT: R 109 TRP cc_start: 0.2452 (m100) cc_final: 0.1812 (m100) REVERT: R 140 MET cc_start: 0.7362 (tmm) cc_final: 0.7069 (tmm) REVERT: R 165 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6751 (pp) REVERT: R 183 ARG cc_start: 0.6059 (OUTLIER) cc_final: 0.5280 (ttm170) REVERT: R 199 PRO cc_start: 0.6375 (Cg_endo) cc_final: 0.6123 (Cg_exo) REVERT: R 203 ASP cc_start: 0.5059 (OUTLIER) cc_final: 0.4585 (p0) REVERT: R 284 THR cc_start: 0.7751 (t) cc_final: 0.7529 (t) REVERT: R 287 TRP cc_start: 0.5983 (m-10) cc_final: 0.5055 (m-10) REVERT: R 300 ARG cc_start: 0.6172 (OUTLIER) cc_final: 0.5727 (mtm110) REVERT: R 395 ILE cc_start: 0.7659 (mm) cc_final: 0.7372 (mm) outliers start: 44 outliers final: 31 residues processed: 202 average time/residue: 0.3034 time to fit residues: 82.5407 Evaluate side-chains 198 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 160 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 203 ASP Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 293 LYS Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain R residue 300 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 0.0980 chunk 88 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 118 optimal weight: 0.7980 chunk 124 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 39 GLN P 19 GLN R 93 HIS R 204 GLN ** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11124 Z= 0.239 Angle : 0.650 12.301 15098 Z= 0.323 Chirality : 0.043 0.182 1673 Planarity : 0.004 0.048 1921 Dihedral : 5.178 59.637 1536 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.37 % Allowed : 18.52 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.23), residues: 1353 helix: 0.90 (0.25), residues: 428 sheet: -1.12 (0.28), residues: 308 loop : -1.30 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 233 HIS 0.004 0.001 HIS A 357 PHE 0.018 0.001 PHE R 270 TYR 0.023 0.002 TYR R 259 ARG 0.008 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 168 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 264 ASN cc_start: 0.6651 (OUTLIER) cc_final: 0.6205 (t0) REVERT: B 19 ARG cc_start: 0.7053 (mtp-110) cc_final: 0.6523 (mtp85) REVERT: B 44 GLN cc_start: 0.6513 (OUTLIER) cc_final: 0.6131 (pm20) REVERT: B 336 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7812 (mp) REVERT: E 128 MET cc_start: 0.7028 (mtm) cc_final: 0.6764 (mtm) REVERT: G 21 MET cc_start: 0.6103 (tmm) cc_final: 0.5807 (tpp) REVERT: G 46 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.6322 (mmtm) REVERT: R 39 TRP cc_start: 0.6807 (t60) cc_final: 0.6341 (t60) REVERT: R 109 TRP cc_start: 0.2419 (m100) cc_final: 0.1744 (m100) REVERT: R 140 MET cc_start: 0.7409 (tmm) cc_final: 0.7110 (tmm) REVERT: R 165 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6675 (pp) REVERT: R 199 PRO cc_start: 0.6412 (Cg_endo) cc_final: 0.6171 (Cg_exo) REVERT: R 203 ASP cc_start: 0.5101 (OUTLIER) cc_final: 0.4581 (p0) REVERT: R 287 TRP cc_start: 0.6097 (m-10) cc_final: 0.4898 (m-10) REVERT: R 300 ARG cc_start: 0.6188 (OUTLIER) cc_final: 0.5737 (mtm110) REVERT: R 395 ILE cc_start: 0.7724 (mm) cc_final: 0.7453 (mm) outliers start: 50 outliers final: 36 residues processed: 208 average time/residue: 0.2761 time to fit residues: 76.5004 Evaluate side-chains 204 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 161 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 203 ASP Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 293 LYS Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain R residue 300 ARG Chi-restraints excluded: chain R residue 301 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN P 19 GLN ** R 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 HIS R 204 GLN ** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11124 Z= 0.296 Angle : 0.676 12.449 15098 Z= 0.341 Chirality : 0.044 0.188 1673 Planarity : 0.005 0.049 1921 Dihedral : 5.335 58.128 1536 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.10 % Allowed : 19.65 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.23), residues: 1353 helix: 0.74 (0.25), residues: 427 sheet: -1.26 (0.28), residues: 321 loop : -1.34 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 233 HIS 0.005 0.001 HIS R 173 PHE 0.019 0.002 PHE R 270 TYR 0.024 0.002 TYR R 259 ARG 0.009 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 162 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7057 (mtp-110) cc_final: 0.6557 (mtp85) REVERT: B 44 GLN cc_start: 0.6535 (OUTLIER) cc_final: 0.6154 (pm20) REVERT: B 211 TRP cc_start: 0.7894 (m100) cc_final: 0.7565 (m100) REVERT: B 336 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7775 (mp) REVERT: G 21 MET cc_start: 0.5976 (tmm) cc_final: 0.5741 (tpp) REVERT: G 46 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6368 (mmtm) REVERT: R 39 TRP cc_start: 0.6775 (t60) cc_final: 0.6336 (t60) REVERT: R 109 TRP cc_start: 0.2362 (m100) cc_final: 0.1716 (m100) REVERT: R 165 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6671 (pp) REVERT: R 199 PRO cc_start: 0.6434 (Cg_endo) cc_final: 0.6170 (Cg_exo) REVERT: R 203 ASP cc_start: 0.5057 (OUTLIER) cc_final: 0.4506 (p0) REVERT: R 287 TRP cc_start: 0.6135 (m-10) cc_final: 0.5024 (m-10) REVERT: R 300 ARG cc_start: 0.6199 (OUTLIER) cc_final: 0.5782 (mtm110) REVERT: R 395 ILE cc_start: 0.7722 (mm) cc_final: 0.7456 (mm) outliers start: 47 outliers final: 34 residues processed: 199 average time/residue: 0.2716 time to fit residues: 72.9975 Evaluate side-chains 196 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 156 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 203 ASP Chi-restraints excluded: chain R residue 293 LYS Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain R residue 300 ARG Chi-restraints excluded: chain R residue 301 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 5.9990 chunk 78 optimal weight: 0.1980 chunk 60 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN P 19 GLN ** R 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 HIS R 204 GLN ** R 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11124 Z= 0.167 Angle : 0.619 12.616 15098 Z= 0.309 Chirality : 0.042 0.181 1673 Planarity : 0.004 0.049 1921 Dihedral : 5.050 58.261 1536 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.67 % Allowed : 19.74 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.23), residues: 1353 helix: 0.97 (0.26), residues: 427 sheet: -1.18 (0.28), residues: 311 loop : -1.21 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 233 HIS 0.003 0.001 HIS E 35 PHE 0.019 0.001 PHE B 253 TYR 0.022 0.002 TYR R 141 ARG 0.007 0.001 ARG E 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 168 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ASN cc_start: 0.6581 (OUTLIER) cc_final: 0.6097 (t0) REVERT: B 19 ARG cc_start: 0.7068 (mtp-110) cc_final: 0.6545 (mtp85) REVERT: B 44 GLN cc_start: 0.6507 (OUTLIER) cc_final: 0.6139 (pm20) REVERT: B 336 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7723 (mp) REVERT: E 130 GLN cc_start: 0.5750 (mm110) cc_final: 0.5212 (mm110) REVERT: G 46 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6330 (mmtm) REVERT: R 39 TRP cc_start: 0.6801 (t60) cc_final: 0.6354 (t60) REVERT: R 109 TRP cc_start: 0.2310 (m100) cc_final: 0.1691 (m100) REVERT: R 165 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6764 (pp) REVERT: R 183 ARG cc_start: 0.6016 (OUTLIER) cc_final: 0.5187 (ttm170) REVERT: R 199 PRO cc_start: 0.6401 (Cg_endo) cc_final: 0.6172 (Cg_exo) REVERT: R 203 ASP cc_start: 0.5009 (OUTLIER) cc_final: 0.4498 (p0) REVERT: R 287 TRP cc_start: 0.6054 (m-10) cc_final: 0.4843 (m-10) REVERT: R 300 ARG cc_start: 0.6155 (OUTLIER) cc_final: 0.5750 (mtm110) REVERT: R 305 MET cc_start: 0.6549 (mmp) cc_final: 0.6128 (mmt) REVERT: R 395 ILE cc_start: 0.7685 (mm) cc_final: 0.7409 (mm) outliers start: 42 outliers final: 29 residues processed: 201 average time/residue: 0.2782 time to fit residues: 75.7865 Evaluate side-chains 197 residues out of total 1174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 141 TYR Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 183 ARG Chi-restraints excluded: chain R residue 203 ASP Chi-restraints excluded: chain R residue 297 TRP Chi-restraints excluded: chain R residue 300 ARG Chi-restraints excluded: chain R residue 301 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN P 19 GLN ** R 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 HIS R 204 GLN ** R 224 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 = 0.4248 r_free = 0.4248 target = 0.168272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.136589 restraints weight = 16013.523| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.26 r_work: 0.3750 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11124 Z= 0.208 Angle : 0.626 12.757 15098 Z= 0.313 Chirality : 0.043 0.186 1673 Planarity : 0.004 0.050 1921 Dihedral : 5.099 59.186 1536 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.49 % Allowed : 20.17 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.23), residues: 1353 helix: 0.95 (0.25), residues: 427 sheet: -1.16 (0.28), residues: 314 loop : -1.22 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 71 HIS 0.003 0.001 HIS A 357 PHE 0.018 0.001 PHE B 253 TYR 0.020 0.002 TYR R 141 ARG 0.007 0.001 ARG E 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2662.49 seconds wall clock time: 49 minutes 52.19 seconds (2992.19 seconds total)