Starting phenix.real_space_refine on Sun Apr 7 21:25:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhg_23339/04_2024/7lhg_23339.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhg_23339/04_2024/7lhg_23339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhg_23339/04_2024/7lhg_23339.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhg_23339/04_2024/7lhg_23339.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhg_23339/04_2024/7lhg_23339.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lhg_23339/04_2024/7lhg_23339.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 32 5.16 5 C 7299 2.51 5 N 2024 2.21 5 O 2237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 54": "OE1" <-> "OE2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 125": "NH1" <-> "NH2" Residue "C ARG 138": "NH1" <-> "NH2" Residue "C ASP 149": "OD1" <-> "OD2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 303": "NH1" <-> "NH2" Residue "C PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 344": "NH1" <-> "NH2" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 445": "OE1" <-> "OE2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "C TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C ARG 499": "NH1" <-> "NH2" Residue "C ASP 502": "OD1" <-> "OD2" Residue "C TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 510": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 542": "NH1" <-> "NH2" Residue "C ARG 596": "NH1" <-> "NH2" Residue "C TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 652": "NH1" <-> "NH2" Residue "C ARG 674": "NH1" <-> "NH2" Residue "C TYR 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 688": "NH1" <-> "NH2" Residue "C ARG 697": "NH1" <-> "NH2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "C ARG 721": "NH1" <-> "NH2" Residue "C PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 12": "OD1" <-> "OD2" Residue "D ASP 21": "OD1" <-> "OD2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 168": "OE1" <-> "OE2" Residue "K PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 117": "OD1" <-> "OD2" Residue "G ASP 133": "OD1" <-> "OD2" Residue "G ASP 163": "OD1" <-> "OD2" Residue "G TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 282": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11592 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 6217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6217 Classifications: {'peptide': 805} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 31, 'TRANS': 773} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1702 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 16, 'TRANS': 198} Chain: "K" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1177 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 146} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2496 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 299} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 6.60, per 1000 atoms: 0.57 Number of scatterers: 11592 At special positions: 0 Unit cell: (99.813, 96.726, 171.843, 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 32 16.00 O 2237 8.00 N 2024 7.00 C 7299 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.22 Conformation dependent library (CDL) restraints added in 2.3 seconds 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2700 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 28 sheets defined 4.2% alpha, 38.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'C' and resid 19 through 25 Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.587A pdb=" N VAL C 76 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.658A pdb=" N LEU C 126 " --> pdb=" O GLN C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 459 removed outlier: 4.111A pdb=" N TYR C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 127 through 132 removed outlier: 3.632A pdb=" N ASP D 130 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 158 Processing helix chain 'G' and resid 194 through 200 Processing helix chain 'G' and resid 232 through 237 Processing sheet with id=AA1, first strand: chain 'C' and resid 31 through 32 removed outlier: 3.730A pdb=" N TYR C 32 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 50 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL C 53 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLN C 68 " --> pdb=" O VAL C 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 41 through 42 removed outlier: 6.609A pdb=" N ASP C 35 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE C 119 " --> pdb=" O ASP C 35 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE C 37 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 116 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP C 111 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG C 118 " --> pdb=" O ARG C 109 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP C 107 " --> pdb=" O ASN C 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 467 through 469 removed outlier: 6.727A pdb=" N THR C 494 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 473 " --> pdb=" O TYR C 490 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR C 471 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR C 472 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA C 439 " --> pdb=" O THR C 472 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR C 474 " --> pdb=" O THR C 437 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 410 " --> pdb=" O ARG C 414 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR C 398 " --> pdb=" O SER C 426 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 393 " --> pdb=" O GLY C 397 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 382 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 343 " --> pdb=" O PHE C 357 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR C 338 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP C 239 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 231 " --> pdb=" O TRP C 239 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR C 241 " --> pdb=" O ASN C 229 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN C 229 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 217 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE C 211 " --> pdb=" O GLU C 228 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N ASN C 230 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 14.993A pdb=" N SER C 209 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU C 192 " --> pdb=" O ASN C 203 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN C 205 " --> pdb=" O SER C 190 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASP C 186 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE C 211 " --> pdb=" O ARG C 184 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ARG C 184 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU C 213 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG C 182 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN C 153 " --> pdb=" O SER C 169 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN C 151 " --> pdb=" O ASN C 171 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR C 634 " --> pdb=" O ALA C 641 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 641 through 643 removed outlier: 3.604A pdb=" N THR C 634 " --> pdb=" O ALA C 641 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 579 " --> pdb=" O SER C 603 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 594 through 595 Processing sheet with id=AA6, first strand: chain 'C' and resid 594 through 595 removed outlier: 3.665A pdb=" N SER C 588 " --> pdb=" O TYR C 563 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 563 " --> pdb=" O SER C 588 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 529 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 491 " --> pdb=" O TYR C 503 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR C 494 " --> pdb=" O LYS C 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 265 through 266 removed outlier: 4.040A pdb=" N GLY C 266 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 293 " --> pdb=" O GLY C 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 277 removed outlier: 4.190A pdb=" N SER C 277 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP C 307 " --> pdb=" O SER C 277 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU C 306 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 322 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 308 " --> pdb=" O PHE C 320 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE C 320 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS C 318 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 677 through 680 removed outlier: 3.710A pdb=" N GLY C 719 " --> pdb=" O ARG C 652 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C 721 " --> pdb=" O LEU C 654 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 689 through 690 removed outlier: 3.542A pdb=" N ASN C 689 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER C 711 " --> pdb=" O ASN C 689 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'C' and resid 730 through 732 Processing sheet with id=AB4, first strand: chain 'C' and resid 756 through 758 removed outlier: 3.642A pdb=" N GLY C 758 " --> pdb=" O VAL C 749 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL C 779 " --> pdb=" O GLN C 786 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN C 786 " --> pdb=" O VAL C 779 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP C 781 " --> pdb=" O LYS C 784 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 2 through 4 removed outlier: 3.568A pdb=" N SER D 3 " --> pdb=" O SER D 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 8 through 12 removed outlier: 6.542A pdb=" N ALA D 9 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ARG D 116 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE D 11 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 56 through 59 removed outlier: 3.624A pdb=" N GLN D 57 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 32 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR D 109 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU D 92 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU D 107 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL D 102 " --> pdb=" O ALA K 169 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ALA K 171 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN D 104 " --> pdb=" O ALA K 171 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE K 173 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA D 106 " --> pdb=" O PHE K 173 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU K 175 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLN D 108 " --> pdb=" O LEU K 175 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N TYR K 177 " --> pdb=" O GLN D 108 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LYS D 110 " --> pdb=" O TYR K 177 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR K 176 " --> pdb=" O THR K 85 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 50 through 52 removed outlier: 4.076A pdb=" N ILE D 51 " --> pdb=" O SER D 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 177 through 181 removed outlier: 3.699A pdb=" N SER D 177 " --> pdb=" O ASN D 145 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE D 133 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 171 through 172 removed outlier: 3.850A pdb=" N VAL D 171 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 153 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR D 152 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE D 194 " --> pdb=" O THR D 152 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N SER D 192 " --> pdb=" O ILE D 154 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 66 through 70 removed outlier: 3.772A pdb=" N GLU K 66 " --> pdb=" O ALA K 148 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA K 148 " --> pdb=" O GLU K 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 110 through 112 Processing sheet with id=AC4, first strand: chain 'G' and resid 57 through 61 removed outlier: 6.914A pdb=" N PHE G 26 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN G 180 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE G 81 " --> pdb=" O GLN G 180 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS G 182 " --> pdb=" O GLU G 79 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU G 79 " --> pdb=" O HIS G 182 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA G 184 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR G 77 " --> pdb=" O ALA G 184 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG G 78 " --> pdb=" O ASP G 128 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP G 128 " --> pdb=" O ARG G 78 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS G 126 " --> pdb=" O TYR G 80 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ALA G 82 " --> pdb=" O GLY G 124 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY G 124 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL G 84 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU G 122 " --> pdb=" O VAL G 84 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE G 120 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 57 through 61 removed outlier: 6.914A pdb=" N PHE G 26 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN G 180 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE G 81 " --> pdb=" O GLN G 180 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS G 182 " --> pdb=" O GLU G 79 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU G 79 " --> pdb=" O HIS G 182 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA G 184 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR G 77 " --> pdb=" O ALA G 184 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 33 through 40 removed outlier: 3.578A pdb=" N TYR G 35 " --> pdb=" O LEU G 208 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU G 210 " --> pdb=" O TYR G 35 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LYS G 212 " --> pdb=" O GLY G 37 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN G 39 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE G 211 " --> pdb=" O TYR G 169 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 47 through 49 removed outlier: 3.600A pdb=" N GLU G 101 " --> pdb=" O LYS G 157 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 240 through 241 Processing sheet with id=AC9, first strand: chain 'G' and resid 240 through 241 Processing sheet with id=AD1, first strand: chain 'G' and resid 256 through 261 removed outlier: 3.523A pdb=" N ARG G 256 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR G 330 " --> pdb=" O LEU G 260 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 915 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: 4.30 Time building geometry restraints manager: 4.63 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: 3737 1.34 - 1.46: 2826 1.46 - 1.58: 5240 1.58 - 1.70: 2 1.70 - 1.83: 52 Bond restraints: 11857 Sorted by residual: bond pdb=" C THR D 71 " pdb=" N THR D 72 " ideal model delta sigma weight residual 1.327 1.480 -0.153 1.71e-02 3.42e+03 8.01e+01 bond pdb=" C LYS D 77 " pdb=" N LEU D 78 " ideal model delta sigma weight residual 1.328 1.398 -0.070 1.14e-02 7.69e+03 3.80e+01 bond pdb=" CA LEU C 86 " pdb=" CB LEU C 86 " ideal model delta sigma weight residual 1.527 1.599 -0.072 1.75e-02 3.27e+03 1.70e+01 bond pdb=" C VAL C 288 " pdb=" N PRO C 289 " ideal model delta sigma weight residual 1.330 1.373 -0.043 1.25e-02 6.40e+03 1.18e+01 bond pdb=" CA CYS K 75 " pdb=" C CYS K 75 " ideal model delta sigma weight residual 1.522 1.565 -0.042 1.37e-02 5.33e+03 9.62e+00 ... (remaining 11852 not shown) Histogram of bond angle deviations from ideal: 97.09 - 107.15: 566 107.15 - 117.21: 7834 117.21 - 127.28: 7537 127.28 - 137.34: 168 137.34 - 147.40: 2 Bond angle restraints: 16107 Sorted by residual: angle pdb=" N ILE C 235 " pdb=" CA ILE C 235 " pdb=" C ILE C 235 " ideal model delta sigma weight residual 111.62 100.76 10.86 7.90e-01 1.60e+00 1.89e+02 angle pdb=" C THR D 71 " pdb=" N THR D 72 " pdb=" CA THR D 72 " ideal model delta sigma weight residual 123.15 147.40 -24.25 2.23e+00 2.01e-01 1.18e+02 angle pdb=" C TYR K 58 " pdb=" N PRO K 59 " pdb=" CA PRO K 59 " ideal model delta sigma weight residual 120.38 131.09 -10.71 1.03e+00 9.43e-01 1.08e+02 angle pdb=" N ASN C 368 " pdb=" CA ASN C 368 " pdb=" C ASN C 368 " ideal model delta sigma weight residual 110.44 99.09 11.35 1.20e+00 6.94e-01 8.94e+01 angle pdb=" CA TYR C 26 " pdb=" CB TYR C 26 " pdb=" CG TYR C 26 " ideal model delta sigma weight residual 113.90 130.59 -16.69 1.80e+00 3.09e-01 8.60e+01 ... (remaining 16102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 6140 17.08 - 34.16: 681 34.16 - 51.24: 145 51.24 - 68.32: 28 68.32 - 85.40: 14 Dihedral angle restraints: 7008 sinusoidal: 2749 harmonic: 4259 Sorted by residual: dihedral pdb=" C ASP C 481 " pdb=" N ASP C 481 " pdb=" CA ASP C 481 " pdb=" CB ASP C 481 " ideal model delta harmonic sigma weight residual -122.60 -133.64 11.04 0 2.50e+00 1.60e-01 1.95e+01 dihedral pdb=" N ASP C 481 " pdb=" C ASP C 481 " pdb=" CA ASP C 481 " pdb=" CB ASP C 481 " ideal model delta harmonic sigma weight residual 122.80 132.58 -9.78 0 2.50e+00 1.60e-01 1.53e+01 dihedral pdb=" C VAL C 7 " pdb=" N VAL C 7 " pdb=" CA VAL C 7 " pdb=" CB VAL C 7 " ideal model delta harmonic sigma weight residual -122.00 -130.96 8.96 0 2.50e+00 1.60e-01 1.28e+01 ... (remaining 7005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1295 0.084 - 0.168: 362 0.168 - 0.252: 66 0.252 - 0.336: 19 0.336 - 0.419: 5 Chirality restraints: 1747 Sorted by residual: chirality pdb=" CA CYS D 207 " pdb=" N CYS D 207 " pdb=" C CYS D 207 " pdb=" CB CYS D 207 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CB ILE D 194 " pdb=" CA ILE D 194 " pdb=" CG1 ILE D 194 " pdb=" CG2 ILE D 194 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA TRP C 92 " pdb=" N TRP C 92 " pdb=" C TRP C 92 " pdb=" CB TRP C 92 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 1744 not shown) Planarity restraints: 2112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 72 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO D 73 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO D 73 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 73 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 327 " 0.061 5.00e-02 4.00e+02 9.26e-02 1.37e+01 pdb=" N PRO C 328 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO C 328 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 328 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 698 " -0.055 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO C 699 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 699 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 699 " -0.045 5.00e-02 4.00e+02 ... (remaining 2109 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3558 2.84 - 3.35: 9196 3.35 - 3.87: 19317 3.87 - 4.38: 19881 4.38 - 4.90: 35363 Nonbonded interactions: 87315 Sorted by model distance: nonbonded pdb=" O ASN G 196 " pdb=" OG1 THR G 200 " model vdw 2.325 2.440 nonbonded pdb=" OG1 THR C 72 " pdb=" OD1 ASP C 74 " model vdw 2.334 2.440 nonbonded pdb=" OG SER C 612 " pdb=" OG SER C 628 " model vdw 2.340 2.440 nonbonded pdb=" OG SER D 159 " pdb=" OE1 GLN D 162 " model vdw 2.345 2.440 nonbonded pdb=" O VAL C 1 " pdb=" OG SER C 22 " model vdw 2.353 2.440 ... (remaining 87310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 2.380 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 33.680 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.008 0.153 11857 Z= 0.507 Angle : 1.665 24.249 16107 Z= 1.009 Chirality : 0.084 0.419 1747 Planarity : 0.009 0.104 2112 Dihedral : 14.921 85.404 4308 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.26 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 14.72 % Favored : 85.28 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.17), residues: 1482 helix: -4.64 (0.30), residues: 52 sheet: -2.41 (0.20), residues: 530 loop : -3.30 (0.15), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 781 HIS 0.026 0.004 HIS K 36 PHE 0.045 0.004 PHE G 209 TYR 0.038 0.004 TYR K 58 ARG 0.027 0.001 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 470 MET cc_start: 0.8237 (ttp) cc_final: 0.7485 (tmm) REVERT: C 790 ASN cc_start: 0.8581 (t0) cc_final: 0.8338 (t0) REVERT: D 7 THR cc_start: 0.8834 (t) cc_final: 0.8633 (m) REVERT: D 87 TYR cc_start: 0.8365 (m-10) cc_final: 0.8145 (m-10) REVERT: D 193 TYR cc_start: 0.8469 (p90) cc_final: 0.8221 (p90) REVERT: D 212 CYS cc_start: 0.8349 (p) cc_final: 0.8006 (p) REVERT: K 30 LEU cc_start: 0.8478 (tp) cc_final: 0.7937 (mp) REVERT: K 66 GLU cc_start: 0.8658 (tp30) cc_final: 0.8400 (tp30) REVERT: K 101 LYS cc_start: 0.9054 (mttm) cc_final: 0.8849 (mmmm) REVERT: K 112 ILE cc_start: 0.9137 (mm) cc_final: 0.8620 (mp) REVERT: K 130 ASN cc_start: 0.8570 (m-40) cc_final: 0.8290 (p0) REVERT: K 174 GLU cc_start: 0.6869 (pm20) cc_final: 0.6303 (pm20) REVERT: G 84 VAL cc_start: 0.7642 (t) cc_final: 0.7418 (t) REVERT: G 269 HIS cc_start: 0.4733 (m-70) cc_final: 0.4445 (m90) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.2942 time to fit residues: 103.5018 Evaluate side-chains 166 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 115 optimal weight: 30.0000 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 HIS ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN K 43 ASN ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 11857 Z= 0.328 Angle : 0.759 10.016 16107 Z= 0.399 Chirality : 0.047 0.201 1747 Planarity : 0.006 0.096 2112 Dihedral : 5.132 55.245 1650 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.62 % Allowed : 19.39 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.19), residues: 1482 helix: -3.26 (0.59), residues: 36 sheet: -2.16 (0.20), residues: 604 loop : -2.65 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 421 HIS 0.010 0.002 HIS G 239 PHE 0.026 0.002 PHE G 209 TYR 0.024 0.002 TYR C 471 ARG 0.009 0.001 ARG C 446 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 163 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 LEU cc_start: 0.8776 (mt) cc_final: 0.8562 (mp) REVERT: C 338 TYR cc_start: 0.9037 (p90) cc_final: 0.8768 (p90) REVERT: C 470 MET cc_start: 0.8143 (ttp) cc_final: 0.7531 (tmm) REVERT: C 790 ASN cc_start: 0.8607 (t0) cc_final: 0.8401 (t0) REVERT: D 87 TYR cc_start: 0.8857 (m-10) cc_final: 0.8612 (m-10) REVERT: D 115 TYR cc_start: 0.8860 (t80) cc_final: 0.8606 (t80) REVERT: D 121 LYS cc_start: 0.9273 (tttt) cc_final: 0.8901 (tptt) REVERT: D 132 LEU cc_start: 0.9243 (mt) cc_final: 0.9014 (mt) REVERT: K 26 PHE cc_start: 0.7731 (p90) cc_final: 0.7417 (p90) REVERT: K 30 LEU cc_start: 0.8829 (tp) cc_final: 0.8235 (mt) REVERT: K 66 GLU cc_start: 0.8950 (tp30) cc_final: 0.8663 (tp30) REVERT: K 112 ILE cc_start: 0.9177 (mm) cc_final: 0.8797 (mp) REVERT: K 130 ASN cc_start: 0.8541 (m-40) cc_final: 0.8254 (p0) REVERT: K 149 TYR cc_start: 0.8688 (p90) cc_final: 0.7766 (p90) REVERT: G 24 ILE cc_start: 0.7416 (mt) cc_final: 0.7134 (mm) outliers start: 45 outliers final: 27 residues processed: 199 average time/residue: 0.2515 time to fit residues: 71.0381 Evaluate side-chains 175 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 209 PHE Chi-restraints excluded: chain G residue 250 ASP Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 291 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 0.0040 chunk 41 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN C 232 ASN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 11857 Z= 0.195 Angle : 0.678 11.572 16107 Z= 0.341 Chirality : 0.045 0.188 1747 Planarity : 0.005 0.068 2112 Dihedral : 4.741 48.013 1650 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.02 % Allowed : 22.77 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.33 (0.20), residues: 1482 helix: -2.70 (0.72), residues: 36 sheet: -1.94 (0.20), residues: 600 loop : -2.43 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 133 HIS 0.020 0.002 HIS G 279 PHE 0.021 0.002 PHE G 209 TYR 0.023 0.002 TYR C 720 ARG 0.008 0.001 ARG G 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 164 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 ARG cc_start: 0.9056 (tmm160) cc_final: 0.8765 (tmm-80) REVERT: C 451 MET cc_start: 0.8880 (tpt) cc_final: 0.8436 (tpp) REVERT: C 470 MET cc_start: 0.8168 (ttp) cc_final: 0.7781 (tmm) REVERT: C 790 ASN cc_start: 0.8612 (t0) cc_final: 0.8391 (t0) REVERT: D 87 TYR cc_start: 0.8807 (m-10) cc_final: 0.8590 (m-10) REVERT: D 92 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8255 (mt-10) REVERT: D 115 TYR cc_start: 0.8847 (t80) cc_final: 0.8556 (t80) REVERT: D 121 LYS cc_start: 0.9300 (tttt) cc_final: 0.8934 (tptt) REVERT: K 26 PHE cc_start: 0.7553 (p90) cc_final: 0.7280 (p90) REVERT: K 30 LEU cc_start: 0.8927 (tp) cc_final: 0.8432 (mp) REVERT: K 66 GLU cc_start: 0.8960 (tp30) cc_final: 0.8660 (tp30) REVERT: K 85 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8539 (p) REVERT: K 92 GLU cc_start: 0.8881 (tt0) cc_final: 0.8660 (tp30) REVERT: K 112 ILE cc_start: 0.9201 (mm) cc_final: 0.8831 (mp) REVERT: K 130 ASN cc_start: 0.8544 (m-40) cc_final: 0.8231 (p0) REVERT: G 48 PHE cc_start: 0.8184 (p90) cc_final: 0.7940 (p90) REVERT: G 49 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.7070 (pt) REVERT: G 56 ILE cc_start: 0.8224 (tt) cc_final: 0.8023 (pt) outliers start: 50 outliers final: 30 residues processed: 206 average time/residue: 0.2381 time to fit residues: 71.0055 Evaluate side-chains 182 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 250 ASP Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 332 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 ASN C 799 GLN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 11857 Z= 0.321 Angle : 0.717 9.952 16107 Z= 0.367 Chirality : 0.047 0.199 1747 Planarity : 0.005 0.085 2112 Dihedral : 4.938 39.084 1650 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 5.55 % Allowed : 22.69 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.20), residues: 1482 helix: -2.35 (0.75), residues: 37 sheet: -1.94 (0.20), residues: 605 loop : -2.23 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 133 HIS 0.010 0.002 HIS G 279 PHE 0.021 0.002 PHE G 209 TYR 0.028 0.002 TYR C 720 ARG 0.010 0.001 ARG K 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 149 time to evaluate : 1.417 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 7 VAL cc_start: 0.7199 (OUTLIER) cc_final: 0.6998 (p) REVERT: C 246 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8905 (tt) REVERT: C 470 MET cc_start: 0.8196 (ttp) cc_final: 0.7773 (ptm) REVERT: C 602 TYR cc_start: 0.8431 (t80) cc_final: 0.8090 (t80) REVERT: C 790 ASN cc_start: 0.8692 (t0) cc_final: 0.8486 (t0) REVERT: D 87 TYR cc_start: 0.8943 (m-10) cc_final: 0.8724 (m-10) REVERT: D 115 TYR cc_start: 0.8929 (t80) cc_final: 0.8690 (t80) REVERT: D 121 LYS cc_start: 0.9282 (tttt) cc_final: 0.8960 (tptt) REVERT: K 66 GLU cc_start: 0.9048 (tp30) cc_final: 0.8733 (tp30) REVERT: K 92 GLU cc_start: 0.8891 (tt0) cc_final: 0.8667 (tp30) REVERT: K 112 ILE cc_start: 0.9200 (mm) cc_final: 0.8819 (mp) REVERT: K 130 ASN cc_start: 0.8583 (m-40) cc_final: 0.8277 (p0) REVERT: G 24 ILE cc_start: 0.8078 (mt) cc_final: 0.7747 (mm) REVERT: G 180 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7982 (pm20) REVERT: G 196 ASN cc_start: 0.7841 (p0) cc_final: 0.7483 (p0) outliers start: 69 outliers final: 44 residues processed: 208 average time/residue: 0.2302 time to fit residues: 69.9030 Evaluate side-chains 188 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 141 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 560 ASN Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 141 TYR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 150 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 138 CYS Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 209 PHE Chi-restraints excluded: chain G residue 250 ASP Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 291 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 105 optimal weight: 30.0000 chunk 58 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 ASN C 232 ASN C 560 ASN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11857 Z= 0.289 Angle : 0.688 10.240 16107 Z= 0.350 Chirality : 0.046 0.177 1747 Planarity : 0.005 0.086 2112 Dihedral : 4.949 35.428 1650 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 5.39 % Allowed : 24.70 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.21), residues: 1482 helix: -2.45 (0.70), residues: 39 sheet: -1.86 (0.20), residues: 601 loop : -2.14 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 133 HIS 0.011 0.002 HIS G 279 PHE 0.031 0.002 PHE G 86 TYR 0.027 0.002 TYR C 720 ARG 0.010 0.001 ARG K 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 147 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8770 (pp) REVERT: C 246 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8874 (tt) REVERT: C 470 MET cc_start: 0.8210 (ttp) cc_final: 0.7834 (tmm) REVERT: C 602 TYR cc_start: 0.8484 (t80) cc_final: 0.8090 (t80) REVERT: D 41 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.7910 (p0) REVERT: D 87 TYR cc_start: 0.8961 (m-10) cc_final: 0.8755 (m-10) REVERT: D 115 TYR cc_start: 0.8980 (t80) cc_final: 0.8768 (t80) REVERT: D 121 LYS cc_start: 0.9289 (tttt) cc_final: 0.8960 (tptt) REVERT: D 134 LEU cc_start: 0.9186 (tp) cc_final: 0.8225 (tp) REVERT: K 30 LEU cc_start: 0.9050 (tp) cc_final: 0.8514 (mm) REVERT: K 66 GLU cc_start: 0.9070 (tp30) cc_final: 0.8769 (tp30) REVERT: K 92 GLU cc_start: 0.8849 (tt0) cc_final: 0.8485 (tp30) REVERT: K 101 LYS cc_start: 0.8913 (mmmm) cc_final: 0.8055 (tptt) REVERT: K 112 ILE cc_start: 0.9205 (mm) cc_final: 0.8815 (mp) REVERT: K 130 ASN cc_start: 0.8601 (m-40) cc_final: 0.8146 (p0) REVERT: G 24 ILE cc_start: 0.8219 (mt) cc_final: 0.7818 (mm) REVERT: G 56 ILE cc_start: 0.8910 (tp) cc_final: 0.8499 (pt) REVERT: G 180 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7878 (pm20) REVERT: G 196 ASN cc_start: 0.7795 (p0) cc_final: 0.7526 (p0) outliers start: 67 outliers final: 46 residues processed: 200 average time/residue: 0.2364 time to fit residues: 68.6815 Evaluate side-chains 188 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 138 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 150 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 250 ASP Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 332 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 142 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 0.0020 chunk 74 optimal weight: 0.0470 chunk 137 optimal weight: 0.0370 overall best weight: 0.8168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 ASN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11857 Z= 0.167 Angle : 0.652 12.786 16107 Z= 0.326 Chirality : 0.045 0.163 1747 Planarity : 0.005 0.068 2112 Dihedral : 4.665 35.492 1650 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.59 % Allowed : 25.42 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.21), residues: 1482 helix: -2.24 (0.75), residues: 39 sheet: -1.70 (0.21), residues: 594 loop : -2.03 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 133 HIS 0.006 0.001 HIS G 228 PHE 0.023 0.002 PHE G 209 TYR 0.018 0.002 TYR C 471 ARG 0.011 0.001 ARG K 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 160 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 232 ASN cc_start: 0.7523 (OUTLIER) cc_final: 0.7278 (p0) REVERT: C 287 MET cc_start: 0.8670 (mmm) cc_final: 0.8384 (mmm) REVERT: C 447 ASN cc_start: 0.8437 (t0) cc_final: 0.7600 (t0) REVERT: C 451 MET cc_start: 0.8801 (tpt) cc_final: 0.8522 (tpp) REVERT: C 470 MET cc_start: 0.8200 (ttp) cc_final: 0.7724 (tmm) REVERT: C 602 TYR cc_start: 0.8497 (t80) cc_final: 0.8081 (t80) REVERT: D 41 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.7984 (p0) REVERT: D 87 TYR cc_start: 0.8883 (m-10) cc_final: 0.8682 (m-10) REVERT: D 121 LYS cc_start: 0.9339 (tttt) cc_final: 0.9008 (tptt) REVERT: D 134 LEU cc_start: 0.9343 (tp) cc_final: 0.7953 (tp) REVERT: K 30 LEU cc_start: 0.9051 (tp) cc_final: 0.8691 (mm) REVERT: K 62 ARG cc_start: 0.8642 (mtm-85) cc_final: 0.8429 (mtm-85) REVERT: K 66 GLU cc_start: 0.9011 (tp30) cc_final: 0.8699 (tp30) REVERT: K 92 GLU cc_start: 0.8813 (tt0) cc_final: 0.8585 (tp30) REVERT: K 112 ILE cc_start: 0.9208 (mm) cc_final: 0.8810 (mp) REVERT: K 130 ASN cc_start: 0.8636 (m-40) cc_final: 0.8210 (p0) REVERT: G 24 ILE cc_start: 0.8086 (mt) cc_final: 0.7706 (mm) REVERT: G 56 ILE cc_start: 0.8703 (tp) cc_final: 0.8365 (pt) REVERT: G 180 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.7721 (pm20) REVERT: G 196 ASN cc_start: 0.7884 (p0) cc_final: 0.7444 (p0) outliers start: 57 outliers final: 36 residues processed: 206 average time/residue: 0.2260 time to fit residues: 67.5470 Evaluate side-chains 181 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 142 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain K residue 150 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 250 ASP Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 291 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 141 optimal weight: 0.0570 chunk 88 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 65 optimal weight: 0.0980 chunk 87 optimal weight: 4.9990 overall best weight: 3.2304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 ASN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11857 Z= 0.289 Angle : 0.697 10.626 16107 Z= 0.354 Chirality : 0.046 0.158 1747 Planarity : 0.005 0.082 2112 Dihedral : 4.866 30.988 1650 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 4.91 % Allowed : 26.07 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.21), residues: 1482 helix: -1.72 (0.80), residues: 39 sheet: -1.72 (0.21), residues: 606 loop : -1.99 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 133 HIS 0.007 0.002 HIS K 36 PHE 0.022 0.002 PHE G 86 TYR 0.023 0.002 TYR C 720 ARG 0.011 0.001 ARG K 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 143 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 ARG cc_start: 0.9168 (tmm160) cc_final: 0.8782 (tmm-80) REVERT: C 393 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8270 (mm) REVERT: C 470 MET cc_start: 0.8221 (ttp) cc_final: 0.7684 (tmm) REVERT: C 602 TYR cc_start: 0.8562 (t80) cc_final: 0.8175 (t80) REVERT: D 41 ASN cc_start: 0.8472 (OUTLIER) cc_final: 0.7911 (p0) REVERT: D 87 TYR cc_start: 0.8967 (m-10) cc_final: 0.8764 (m-10) REVERT: D 121 LYS cc_start: 0.9312 (tttt) cc_final: 0.8982 (tptt) REVERT: K 30 LEU cc_start: 0.9139 (tp) cc_final: 0.8869 (mm) REVERT: K 62 ARG cc_start: 0.8698 (mtm-85) cc_final: 0.8480 (mtm-85) REVERT: K 66 GLU cc_start: 0.9084 (tp30) cc_final: 0.8775 (tp30) REVERT: K 92 GLU cc_start: 0.8707 (tt0) cc_final: 0.8370 (tp30) REVERT: K 101 LYS cc_start: 0.8831 (mmmm) cc_final: 0.7897 (tptt) REVERT: K 112 ILE cc_start: 0.9197 (mm) cc_final: 0.8795 (mp) REVERT: K 130 ASN cc_start: 0.8620 (m-40) cc_final: 0.8183 (p0) REVERT: G 24 ILE cc_start: 0.8291 (mt) cc_final: 0.7897 (mm) REVERT: G 56 ILE cc_start: 0.8907 (tp) cc_final: 0.8526 (pt) REVERT: G 180 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: G 196 ASN cc_start: 0.7835 (p0) cc_final: 0.7408 (p0) REVERT: G 299 TRP cc_start: 0.7950 (m-10) cc_final: 0.7208 (m-10) outliers start: 61 outliers final: 45 residues processed: 195 average time/residue: 0.2347 time to fit residues: 66.0606 Evaluate side-chains 185 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 137 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 150 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 228 HIS Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 250 ASP Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 295 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 111 optimal weight: 30.0000 chunk 128 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 ASN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11857 Z= 0.272 Angle : 0.693 13.517 16107 Z= 0.350 Chirality : 0.046 0.210 1747 Planarity : 0.005 0.083 2112 Dihedral : 4.903 29.257 1650 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 5.07 % Allowed : 26.07 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.21), residues: 1482 helix: -2.46 (0.64), residues: 46 sheet: -1.66 (0.21), residues: 606 loop : -2.02 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 133 HIS 0.013 0.002 HIS K 36 PHE 0.021 0.002 PHE G 86 TYR 0.022 0.002 TYR C 720 ARG 0.011 0.001 ARG K 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 140 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.8763 (ptp) cc_final: 0.8404 (pmm) REVERT: C 77 ARG cc_start: 0.9146 (tmm160) cc_final: 0.8786 (tmm-80) REVERT: C 252 MET cc_start: 0.8630 (mmm) cc_final: 0.8426 (mmt) REVERT: C 392 ASP cc_start: 0.7194 (t0) cc_final: 0.6733 (t0) REVERT: C 393 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8103 (mm) REVERT: C 470 MET cc_start: 0.8237 (ttp) cc_final: 0.7705 (tmm) REVERT: C 602 TYR cc_start: 0.8557 (t80) cc_final: 0.8168 (t80) REVERT: D 41 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.7942 (p0) REVERT: D 121 LYS cc_start: 0.9300 (tttt) cc_final: 0.8969 (tptt) REVERT: K 30 LEU cc_start: 0.9110 (tp) cc_final: 0.8627 (mm) REVERT: K 62 ARG cc_start: 0.8732 (mtm-85) cc_final: 0.8508 (mtm-85) REVERT: K 66 GLU cc_start: 0.9128 (tp30) cc_final: 0.8807 (tp30) REVERT: K 92 GLU cc_start: 0.8694 (tt0) cc_final: 0.8398 (tp30) REVERT: K 101 LYS cc_start: 0.8978 (mmmm) cc_final: 0.8081 (tptt) REVERT: K 112 ILE cc_start: 0.9193 (mm) cc_final: 0.8784 (mp) REVERT: K 130 ASN cc_start: 0.8509 (m-40) cc_final: 0.8038 (p0) REVERT: G 24 ILE cc_start: 0.8306 (mt) cc_final: 0.7903 (mm) REVERT: G 56 ILE cc_start: 0.8955 (tp) cc_final: 0.8527 (pt) REVERT: G 180 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8097 (pm20) REVERT: G 196 ASN cc_start: 0.7896 (p0) cc_final: 0.7475 (p0) outliers start: 63 outliers final: 53 residues processed: 195 average time/residue: 0.2430 time to fit residues: 68.4975 Evaluate side-chains 189 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 133 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 560 ASN Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 150 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 228 HIS Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 250 ASP Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 295 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 0.0270 chunk 132 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 overall best weight: 1.4240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 ASN D 135 ASN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11857 Z= 0.186 Angle : 0.681 20.078 16107 Z= 0.337 Chirality : 0.045 0.204 1747 Planarity : 0.005 0.070 2112 Dihedral : 4.734 28.289 1650 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 4.42 % Allowed : 26.95 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.21), residues: 1482 helix: -2.31 (0.66), residues: 46 sheet: -1.59 (0.21), residues: 596 loop : -1.94 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 133 HIS 0.010 0.002 HIS K 36 PHE 0.049 0.002 PHE K 26 TYR 0.019 0.002 TYR C 720 ARG 0.013 0.001 ARG K 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 137 time to evaluate : 1.328 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 75 MET cc_start: 0.8710 (ptp) cc_final: 0.8179 (pmm) REVERT: C 77 ARG cc_start: 0.9132 (tmm160) cc_final: 0.8786 (tmm-80) REVERT: C 287 MET cc_start: 0.8564 (mmm) cc_final: 0.8139 (mmm) REVERT: C 392 ASP cc_start: 0.7034 (t0) cc_final: 0.6636 (t0) REVERT: C 393 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8173 (mm) REVERT: C 470 MET cc_start: 0.8218 (ttp) cc_final: 0.7725 (tmm) REVERT: C 602 TYR cc_start: 0.8529 (t80) cc_final: 0.8117 (t80) REVERT: D 41 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.7984 (p0) REVERT: D 121 LYS cc_start: 0.9304 (tttt) cc_final: 0.8971 (tptt) REVERT: D 172 MET cc_start: 0.8187 (tpt) cc_final: 0.7959 (tpt) REVERT: D 193 TYR cc_start: 0.8894 (p90) cc_final: 0.8509 (p90) REVERT: K 30 LEU cc_start: 0.9031 (tp) cc_final: 0.8745 (mm) REVERT: K 62 ARG cc_start: 0.8717 (mtm-85) cc_final: 0.8482 (mtm-85) REVERT: K 66 GLU cc_start: 0.9080 (tp30) cc_final: 0.8773 (tp30) REVERT: K 92 GLU cc_start: 0.8676 (tt0) cc_final: 0.8387 (tp30) REVERT: K 101 LYS cc_start: 0.8973 (mmmm) cc_final: 0.8096 (tptt) REVERT: K 112 ILE cc_start: 0.9187 (mm) cc_final: 0.8779 (mp) REVERT: K 130 ASN cc_start: 0.8562 (m-40) cc_final: 0.8071 (p0) REVERT: G 24 ILE cc_start: 0.8188 (mt) cc_final: 0.7813 (mm) REVERT: G 56 ILE cc_start: 0.8816 (tp) cc_final: 0.8412 (pt) REVERT: G 180 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7915 (pm20) REVERT: G 196 ASN cc_start: 0.7846 (p0) cc_final: 0.7419 (p0) outliers start: 55 outliers final: 44 residues processed: 181 average time/residue: 0.2440 time to fit residues: 64.2666 Evaluate side-chains 179 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 132 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 150 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 250 ASP Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 291 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 97 optimal weight: 6.9990 chunk 146 optimal weight: 0.0970 chunk 134 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 overall best weight: 1.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 ASN C 610 ASN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11857 Z= 0.180 Angle : 0.679 20.484 16107 Z= 0.335 Chirality : 0.045 0.193 1747 Planarity : 0.005 0.064 2112 Dihedral : 4.630 26.211 1650 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.02 % Allowed : 27.76 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.21), residues: 1482 helix: -2.40 (0.62), residues: 46 sheet: -1.57 (0.21), residues: 606 loop : -1.92 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP C 133 HIS 0.009 0.002 HIS K 36 PHE 0.018 0.002 PHE G 209 TYR 0.018 0.002 TYR C 471 ARG 0.014 0.001 ARG K 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 145 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.8660 (ptp) cc_final: 0.8343 (pmm) REVERT: C 77 ARG cc_start: 0.9069 (tmm160) cc_final: 0.8705 (tmm-80) REVERT: C 287 MET cc_start: 0.8553 (mmm) cc_final: 0.8161 (mmm) REVERT: C 392 ASP cc_start: 0.6990 (t0) cc_final: 0.6638 (t0) REVERT: C 393 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8196 (mm) REVERT: C 447 ASN cc_start: 0.8434 (t0) cc_final: 0.7674 (t0) REVERT: C 449 MET cc_start: 0.8086 (tpp) cc_final: 0.7767 (tmm) REVERT: C 451 MET cc_start: 0.8984 (mmm) cc_final: 0.8448 (tpp) REVERT: C 470 MET cc_start: 0.8216 (ttp) cc_final: 0.7719 (tmm) REVERT: C 602 TYR cc_start: 0.8544 (t80) cc_final: 0.8125 (t80) REVERT: D 41 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.7968 (p0) REVERT: D 121 LYS cc_start: 0.9300 (tttt) cc_final: 0.8984 (tptt) REVERT: D 193 TYR cc_start: 0.8899 (p90) cc_final: 0.8490 (p90) REVERT: K 30 LEU cc_start: 0.9018 (tp) cc_final: 0.8716 (mm) REVERT: K 62 ARG cc_start: 0.8696 (mtm-85) cc_final: 0.8454 (mtm-85) REVERT: K 66 GLU cc_start: 0.9065 (tp30) cc_final: 0.8762 (tp30) REVERT: K 92 GLU cc_start: 0.8658 (tt0) cc_final: 0.8387 (tp30) REVERT: K 101 LYS cc_start: 0.8972 (mmmm) cc_final: 0.8112 (tptt) REVERT: K 112 ILE cc_start: 0.9206 (mm) cc_final: 0.8811 (mp) REVERT: G 24 ILE cc_start: 0.8183 (mt) cc_final: 0.7768 (mm) REVERT: G 180 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7960 (pm20) REVERT: G 196 ASN cc_start: 0.7832 (p0) cc_final: 0.7407 (p0) outliers start: 50 outliers final: 46 residues processed: 187 average time/residue: 0.2511 time to fit residues: 67.6201 Evaluate side-chains 185 residues out of total 1248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 136 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 560 ASN Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 776 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 39 ASN Chi-restraints excluded: chain D residue 41 ASN Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 150 VAL Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 250 ASP Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 291 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 0.0870 chunk 116 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 0.2980 chunk 102 optimal weight: 6.9990 overall best weight: 1.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 ASN D 179 GLN ** G 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.110950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.088718 restraints weight = 36031.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.091677 restraints weight = 18157.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.093586 restraints weight = 11444.058| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11857 Z= 0.165 Angle : 0.666 18.592 16107 Z= 0.326 Chirality : 0.045 0.187 1747 Planarity : 0.004 0.060 2112 Dihedral : 4.538 23.708 1650 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.94 % Allowed : 27.76 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.21), residues: 1482 helix: -2.33 (0.63), residues: 46 sheet: -1.46 (0.21), residues: 591 loop : -1.84 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 133 HIS 0.009 0.002 HIS K 36 PHE 0.016 0.001 PHE G 209 TYR 0.020 0.002 TYR D 141 ARG 0.015 0.001 ARG K 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2592.95 seconds wall clock time: 48 minutes 18.11 seconds (2898.11 seconds total)