Starting phenix.real_space_refine on Mon Aug 5 03:08:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8q_44352/08_2024/9b8q_44352.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8q_44352/08_2024/9b8q_44352.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/9b8q_44352/08_2024/9b8q_44352.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8q_44352/08_2024/9b8q_44352.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8q_44352/08_2024/9b8q_44352.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b8q_44352/08_2024/9b8q_44352.cif" } 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= 0.021 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 45 5.16 5 C 7579 2.51 5 N 2356 2.21 5 O 2368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I GLU 28": "OE1" <-> "OE2" Residue "I GLU 65": "OE1" <-> "OE2" Residue "J TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 97": "OE1" <-> "OE2" Residue "K GLU 55": "OE1" <-> "OE2" Residue "M GLU 45": "OE1" <-> "OE2" Residue "N GLU 20": "OE1" <-> "OE2" Residue "N GLU 52": "OE1" <-> "OE2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "O GLU 93": "OE1" <-> "OE2" Residue "a GLU 178": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12348 Number of models: 1 Model: "" Number of chains: 9 Chain: "G" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2155 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 260} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 363} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 912 Unresolved non-hydrogen angles: 1152 Unresolved non-hydrogen dihedrals: 752 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLN:plan1': 14, 'ARG:plan': 11, 'TYR:plan': 9, 'ASN:plan1': 20, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 7, 'GLU:plan': 21, 'ASP:plan': 22} Unresolved non-hydrogen planarities: 478 Chain: "I" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1087 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 1, 'TRANS': 146} Chain breaks: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "J" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1171 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 147} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 914 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 1, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 10, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 111 Chain: "M" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 740 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'TRANS': 101} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 52 Chain: "N" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 825 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 104} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "O" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 625 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'TRANS': 102} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 144 Chain: "T" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 2136 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 388} Link IDs: {'PTRANS': 8, 'TRANS': 421} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 1462 Unresolved non-hydrogen angles: 1859 Unresolved non-hydrogen dihedrals: 1236 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 34, 'HIS:plan': 11, 'TYR:plan': 17, 'ASN:plan1': 19, 'TRP:plan': 8, 'ASP:plan': 19, 'PHE:plan': 17, 'GLU:plan': 38, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 860 Chain: "a" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2695 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 7.94, per 1000 atoms: 0.64 Number of scatterers: 12348 At special positions: 0 Unit cell: (156.56, 175.1, 188.49, 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 45 16.00 O 2368 8.00 N 2356 7.00 C 7579 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: 5.37 Conformation dependent library (CDL) restraints added in 2.7 seconds 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3644 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 79.1% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'G' and resid 14 through 30 removed outlier: 3.860A pdb=" N THR G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LYS G 21 " --> pdb=" O GLN G 17 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 80 removed outlier: 3.704A pdb=" N ALA G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 84 removed outlier: 3.881A pdb=" N LYS G 84 " --> pdb=" O GLU G 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 81 through 84' Processing helix chain 'G' and resid 97 through 104 Processing helix chain 'G' and resid 117 through 158 removed outlier: 3.525A pdb=" N ILE G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY G 128 " --> pdb=" O ILE G 124 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA G 140 " --> pdb=" O LEU G 136 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER G 141 " --> pdb=" O LYS G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 170 removed outlier: 3.503A pdb=" N VAL G 170 " --> pdb=" O ALA G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 203 Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 254 through 310 removed outlier: 4.177A pdb=" N GLY G 277 " --> pdb=" O LYS G 273 " (cutoff:3.500A) Proline residue: G 278 - end of helix removed outlier: 3.848A pdb=" N SER G 288 " --> pdb=" O LYS G 284 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU G 289 " --> pdb=" O VAL G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 339 Processing helix chain 'I' and resid 4 through 108 removed outlier: 3.641A pdb=" N LYS I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS I 107 " --> pdb=" O SER I 103 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP I 108 " --> pdb=" O LYS I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 119 Processing helix chain 'I' and resid 195 through 216 removed outlier: 3.511A pdb=" N GLN I 206 " --> pdb=" O LEU I 202 " (cutoff:3.500A) Proline residue: I 209 - end of helix Processing helix chain 'J' and resid 5 through 106 Processing helix chain 'J' and resid 108 through 122 removed outlier: 3.751A pdb=" N VAL J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 217 removed outlier: 4.097A pdb=" N ASP J 201 " --> pdb=" O GLU J 197 " (cutoff:3.500A) Proline residue: J 209 - end of helix Processing helix chain 'K' and resid 4 through 105 removed outlier: 3.632A pdb=" N GLN K 11 " --> pdb=" O ASP K 7 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE K 38 " --> pdb=" O ALA K 34 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS K 104 " --> pdb=" O GLN K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 217 removed outlier: 3.692A pdb=" N GLN K 206 " --> pdb=" O LEU K 202 " (cutoff:3.500A) Proline residue: K 209 - end of helix Processing helix chain 'M' and resid 4 through 62 removed outlier: 3.955A pdb=" N LYS M 34 " --> pdb=" O ALA M 30 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLN M 41 " --> pdb=" O LYS M 37 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N MET M 42 " --> pdb=" O GLU M 38 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU M 43 " --> pdb=" O GLU M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 104 removed outlier: 3.973A pdb=" N ASN M 68 " --> pdb=" O GLY M 64 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLU M 93 " --> pdb=" O GLN M 89 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ARG M 94 " --> pdb=" O ARG M 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 105 removed outlier: 3.545A pdb=" N ALA N 25 " --> pdb=" O LYS N 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG N 90 " --> pdb=" O SER N 86 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN N 91 " --> pdb=" O SER N 87 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLU N 93 " --> pdb=" O GLN N 89 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ARG N 94 " --> pdb=" O ARG N 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 105 removed outlier: 3.665A pdb=" N ALA O 14 " --> pdb=" O GLN O 10 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL O 22 " --> pdb=" O ALA O 18 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU O 69 " --> pdb=" O SER O 65 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN O 91 " --> pdb=" O SER O 87 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU O 93 " --> pdb=" O GLN O 89 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ARG O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 29 Processing helix chain 'T' and resid 33 through 39 removed outlier: 3.757A pdb=" N LEU T 37 " --> pdb=" O TRP T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 56 Processing helix chain 'T' and resid 58 through 69 Processing helix chain 'T' and resid 69 through 84 removed outlier: 3.997A pdb=" N ALA T 74 " --> pdb=" O GLY T 70 " (cutoff:3.500A) Processing helix chain 'T' and resid 86 through 104 removed outlier: 3.801A pdb=" N VAL T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 107 through 119 removed outlier: 3.941A pdb=" N PHE T 111 " --> pdb=" O ARG T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 132 Processing helix chain 'T' and resid 134 through 152 Processing helix chain 'T' and resid 158 through 174 Processing helix chain 'T' and resid 193 through 210 Processing helix chain 'T' and resid 211 through 221 removed outlier: 3.661A pdb=" N ARG T 215 " --> pdb=" O VAL T 211 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE T 216 " --> pdb=" O ASN T 212 " (cutoff:3.500A) Processing helix chain 'T' and resid 222 through 233 Processing helix chain 'T' and resid 236 through 251 Processing helix chain 'T' and resid 253 through 260 Processing helix chain 'T' and resid 261 through 263 No H-bonds generated for 'chain 'T' and resid 261 through 263' Processing helix chain 'T' and resid 264 through 276 removed outlier: 4.438A pdb=" N VAL T 268 " --> pdb=" O ASN T 264 " (cutoff:3.500A) Processing helix chain 'T' and resid 278 through 295 Processing helix chain 'T' and resid 298 through 312 Processing helix chain 'T' and resid 313 through 324 removed outlier: 3.949A pdb=" N GLN T 317 " --> pdb=" O LYS T 313 " (cutoff:3.500A) Processing helix chain 'T' and resid 328 through 350 removed outlier: 3.628A pdb=" N SER T 332 " --> pdb=" O ASP T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 351 through 362 Processing helix chain 'T' and resid 367 through 371 Processing helix chain 'T' and resid 372 through 380 Processing helix chain 'T' and resid 381 through 383 No H-bonds generated for 'chain 'T' and resid 381 through 383' Processing helix chain 'T' and resid 384 through 401 removed outlier: 5.135A pdb=" N LEU T 390 " --> pdb=" O LYS T 386 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU T 391 " --> pdb=" O ASN T 387 " (cutoff:3.500A) Processing helix chain 'T' and resid 403 through 421 Processing helix chain 'T' and resid 423 through 432 removed outlier: 4.529A pdb=" N VAL T 427 " --> pdb=" O ARG T 423 " (cutoff:3.500A) Processing helix chain 'T' and resid 432 through 442 removed outlier: 4.049A pdb=" N HIS T 442 " --> pdb=" O MET T 438 " (cutoff:3.500A) Processing helix chain 'T' and resid 445 through 460 removed outlier: 3.554A pdb=" N ASN T 451 " --> pdb=" O GLN T 447 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 33 removed outlier: 4.071A pdb=" N TYR a 23 " --> pdb=" O SER a 19 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N CYS a 24 " --> pdb=" O GLU a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 50 removed outlier: 7.841A pdb=" N LYS a 50 " --> pdb=" O PHE a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 75 Processing helix chain 'a' and resid 92 through 139 removed outlier: 4.398A pdb=" N ASP a 96 " --> pdb=" O ARG a 92 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU a 108 " --> pdb=" O ILE a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 179 through 191 Processing helix chain 'a' and resid 226 through 240 Processing helix chain 'a' and resid 250 through 309 removed outlier: 3.676A pdb=" N ASN a 289 " --> pdb=" O ALA a 285 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ARG a 291 " --> pdb=" O ALA a 287 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL a 292 " --> pdb=" O LYS a 288 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU a 309 " --> pdb=" O HIS a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 329 through 345 Processing sheet with id=AA1, first strand: chain 'G' and resid 33 through 37 Processing sheet with id=AA2, first strand: chain 'G' and resid 182 through 185 removed outlier: 6.498A pdb=" N ASN G 226 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL G 215 " --> pdb=" O ASN G 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 36 through 37 Processing sheet with id=AA4, first strand: chain 'a' and resid 169 through 176 removed outlier: 7.891A pdb=" N VAL a 215 " --> pdb=" O ASN a 204 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASN a 204 " --> pdb=" O VAL a 215 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS a 217 " --> pdb=" O ILE a 202 " (cutoff:3.500A) 1225 hydrogen bonds defined for protein. 3636 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: 4.04 Time building geometry restraints manager: 5.85 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: 4551 1.34 - 1.46: 1413 1.46 - 1.57: 6381 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 12423 Sorted by residual: bond pdb=" C ARG O 17 " pdb=" N ALA O 18 " ideal model delta sigma weight residual 1.335 1.559 -0.224 1.31e-02 5.83e+03 2.91e+02 bond pdb=" CA PHE G 316 " pdb=" C PHE G 316 " ideal model delta sigma weight residual 1.530 1.510 0.020 1.23e-02 6.61e+03 2.68e+00 bond pdb=" CA ILE T 266 " pdb=" CB ILE T 266 " ideal model delta sigma weight residual 1.537 1.521 0.017 1.29e-02 6.01e+03 1.66e+00 bond pdb=" CB PHE G 316 " pdb=" CG PHE G 316 " ideal model delta sigma weight residual 1.502 1.473 0.029 2.30e-02 1.89e+03 1.61e+00 bond pdb=" CB LEU G 300 " pdb=" CG LEU G 300 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.57e+00 ... (remaining 12418 not shown) Histogram of bond angle deviations from ideal: 98.01 - 105.21: 106 105.21 - 112.41: 6556 112.41 - 119.61: 4064 119.61 - 126.81: 6132 126.81 - 134.01: 42 Bond angle restraints: 16900 Sorted by residual: angle pdb=" C ARG O 17 " pdb=" N ALA O 18 " pdb=" CA ALA O 18 " ideal model delta sigma weight residual 120.28 126.58 -6.30 1.34e+00 5.57e-01 2.21e+01 angle pdb=" C LEU G 54 " pdb=" N SER G 55 " pdb=" CA SER G 55 " ideal model delta sigma weight residual 121.18 116.17 5.01 1.98e+00 2.55e-01 6.41e+00 angle pdb=" CA VAL T 277 " pdb=" C VAL T 277 " pdb=" N LYS T 278 " ideal model delta sigma weight residual 116.60 120.12 -3.52 1.45e+00 4.76e-01 5.88e+00 angle pdb=" N THR G 103 " pdb=" CA THR G 103 " pdb=" CB THR G 103 " ideal model delta sigma weight residual 110.22 113.88 -3.66 1.54e+00 4.22e-01 5.63e+00 angle pdb=" N VAL a 323 " pdb=" CA VAL a 323 " pdb=" C VAL a 323 " ideal model delta sigma weight residual 108.06 111.03 -2.97 1.28e+00 6.10e-01 5.39e+00 ... (remaining 16895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6806 17.90 - 35.81: 636 35.81 - 53.71: 154 53.71 - 71.61: 34 71.61 - 89.52: 15 Dihedral angle restraints: 7645 sinusoidal: 2111 harmonic: 5534 Sorted by residual: dihedral pdb=" CA VAL a 323 " pdb=" C VAL a 323 " pdb=" N TRP a 324 " pdb=" CA TRP a 324 " ideal model delta harmonic sigma weight residual 180.00 157.82 22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA CYS a 191 " pdb=" C CYS a 191 " pdb=" N ARG a 192 " pdb=" CA ARG a 192 " ideal model delta harmonic sigma weight residual -180.00 -158.70 -21.30 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA LEU G 58 " pdb=" C LEU G 58 " pdb=" N ALA G 59 " pdb=" CA ALA G 59 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 7642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1465 0.032 - 0.064: 418 0.064 - 0.095: 140 0.095 - 0.127: 33 0.127 - 0.159: 9 Chirality restraints: 2065 Sorted by residual: chirality pdb=" CA ILE a 221 " pdb=" N ILE a 221 " pdb=" C ILE a 221 " pdb=" CB ILE a 221 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA ILE a 320 " pdb=" N ILE a 320 " pdb=" C ILE a 320 " pdb=" CB ILE a 320 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CB THR M 77 " pdb=" CA THR M 77 " pdb=" OG1 THR M 77 " pdb=" CG2 THR M 77 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 2062 not shown) Planarity restraints: 2306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 104 " -0.252 9.50e-02 1.11e+02 1.13e-01 8.81e+00 pdb=" NE ARG G 104 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG G 104 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG G 104 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG G 104 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG N 107 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO N 108 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO N 108 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO N 108 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG a 66 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C ARG a 66 " 0.028 2.00e-02 2.50e+03 pdb=" O ARG a 66 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE a 67 " -0.009 2.00e-02 2.50e+03 ... (remaining 2303 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 127 2.61 - 3.18: 12207 3.18 - 3.75: 19957 3.75 - 4.33: 22017 4.33 - 4.90: 37332 Nonbonded interactions: 91640 Sorted by model distance: nonbonded pdb=" O LEU J 215 " pdb=" OG SER N 87 " model vdw 2.034 3.040 nonbonded pdb=" O THR J 195 " pdb=" OG SER J 198 " model vdw 2.042 3.040 nonbonded pdb=" OH TYR K 57 " pdb=" O ARG O 48 " model vdw 2.049 3.040 nonbonded pdb=" O ASP a 329 " pdb=" OG SER a 332 " model vdw 2.154 3.040 nonbonded pdb=" OE1 GLN a 316 " pdb=" N LYS a 317 " model vdw 2.154 3.120 ... (remaining 91635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'I' and ((resid 4 through 42 and (name N or name CA or name C or name O o \ r name CB )) or resid 43 or (resid 44 through 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 105 or resid 118 or resid 193 thro \ ugh 221)) selection = (chain 'J' and ((resid 4 through 42 and (name N or name CA or name C or name O o \ r name CB )) or resid 43 or (resid 44 through 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 96 or (resid 97 through 105 and (n \ ame N or name CA or name C or name O or name CB )) or resid 118 or resid 193 thr \ ough 221)) selection = (chain 'K' and (resid 4 through 105 or resid 180 or resid 193 through 221)) } ncs_group { reference = (chain 'M' and ((resid 4 through 63 and (name N or name CA or name C or name O o \ r name CB )) or resid 64 through 104)) selection = (chain 'N' and ((resid 4 through 63 and (name N or name CA or name C or name O o \ r name CB )) or resid 64 through 104)) selection = (chain 'O' and ((resid 4 through 72 and (name N or name CA or name C or name O o \ r name CB )) or resid 73 through 104)) } 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.230 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 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 : 0.005 0.224 12423 Z= 0.318 Angle : 0.616 7.852 16900 Z= 0.371 Chirality : 0.036 0.159 2065 Planarity : 0.005 0.113 2306 Dihedral : 16.286 89.518 4001 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.26 % Favored : 95.69 % Rotamer: Outliers : 3.66 % Allowed : 25.24 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 2.27 (0.20), residues: 1856 helix: 2.25 (0.13), residues: 1420 sheet: 0.52 (0.56), residues: 93 loop : -1.51 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP a 324 HIS 0.003 0.001 HIS a 305 PHE 0.020 0.002 PHE a 196 TYR 0.012 0.001 TYR I 57 ARG 0.017 0.001 ARG G 104 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 221 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 301 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6668 (ttt180) REVERT: G 306 SER cc_start: 0.6361 (p) cc_final: 0.5744 (p) REVERT: I 26 LYS cc_start: 0.8447 (mmmt) cc_final: 0.7656 (tppt) REVERT: I 37 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7658 (tp30) REVERT: I 54 MET cc_start: 0.8014 (mmm) cc_final: 0.7298 (mmm) REVERT: J 54 MET cc_start: 0.7544 (mtt) cc_final: 0.7289 (mtt) REVERT: J 197 GLU cc_start: 0.7831 (mp0) cc_final: 0.7451 (mt-10) REVERT: K 66 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7315 (tt0) REVERT: K 76 MET cc_start: 0.8000 (mmt) cc_final: 0.7585 (tpp) REVERT: K 212 ARG cc_start: 0.7996 (ttt-90) cc_final: 0.6972 (ttm170) REVERT: M 42 MET cc_start: 0.8054 (mmm) cc_final: 0.7463 (tmm) REVERT: M 84 MET cc_start: 0.6463 (mtt) cc_final: 0.6212 (mtt) outliers start: 30 outliers final: 22 residues processed: 238 average time/residue: 0.2506 time to fit residues: 84.2187 Evaluate side-chains 225 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 202 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 301 ARG Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 205 GLN Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 52 GLU Chi-restraints excluded: chain N residue 88 GLN Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain a residue 12 LEU Chi-restraints excluded: chain a residue 261 VAL Chi-restraints excluded: chain a residue 303 ILE Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 351 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 3.9990 chunk 139 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 71 GLN a 14 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12423 Z= 0.246 Angle : 0.545 9.673 16900 Z= 0.295 Chirality : 0.036 0.160 2065 Planarity : 0.003 0.041 2306 Dihedral : 5.726 77.152 2017 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.26 % Favored : 97.68 % Rotamer: Outliers : 5.98 % Allowed : 22.32 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 3.12 (0.20), residues: 1856 helix: 2.85 (0.13), residues: 1428 sheet: 0.55 (0.57), residues: 89 loop : -1.18 (0.37), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP a 324 HIS 0.002 0.000 HIS a 343 PHE 0.050 0.002 PHE G 316 TYR 0.017 0.002 TYR I 57 ARG 0.007 0.001 ARG a 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 215 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 26 LYS cc_start: 0.8387 (mmmt) cc_final: 0.7525 (tppt) REVERT: I 37 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7747 (tp30) REVERT: I 54 MET cc_start: 0.8306 (mmm) cc_final: 0.7540 (mmm) REVERT: I 62 LYS cc_start: 0.9219 (tppt) cc_final: 0.8791 (ttmt) REVERT: J 54 MET cc_start: 0.8039 (mtt) cc_final: 0.7817 (mtt) REVERT: K 66 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7242 (tt0) REVERT: K 76 MET cc_start: 0.7822 (mmt) cc_final: 0.7440 (tpp) REVERT: K 212 ARG cc_start: 0.7872 (ttt-90) cc_final: 0.6839 (ttm170) REVERT: M 42 MET cc_start: 0.7869 (mmm) cc_final: 0.7464 (tpt) REVERT: M 50 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7950 (tp30) REVERT: M 84 MET cc_start: 0.6294 (mtt) cc_final: 0.6086 (mtt) REVERT: N 51 ARG cc_start: 0.7983 (mtp180) cc_final: 0.7638 (tpt-90) REVERT: N 88 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7655 (pp30) REVERT: a 209 PRO cc_start: 0.8891 (Cg_endo) cc_final: 0.8642 (Cg_exo) REVERT: a 243 SER cc_start: 0.7456 (OUTLIER) cc_final: 0.7086 (t) outliers start: 49 outliers final: 28 residues processed: 241 average time/residue: 0.2424 time to fit residues: 83.0916 Evaluate side-chains 223 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain a residue 58 CYS Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 218 SER Chi-restraints excluded: chain a residue 243 SER Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 261 VAL Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 341 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 167 optimal weight: 0.5980 chunk 180 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 63 GLN N 10 GLN a 14 GLN a 225 GLN ** a 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12423 Z= 0.290 Angle : 0.566 8.988 16900 Z= 0.304 Chirality : 0.037 0.160 2065 Planarity : 0.003 0.033 2306 Dihedral : 4.667 46.927 1985 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 7.32 % Allowed : 25.12 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 3.00 (0.20), residues: 1856 helix: 2.79 (0.13), residues: 1430 sheet: 0.76 (0.67), residues: 66 loop : -1.27 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP a 324 HIS 0.003 0.001 HIS a 343 PHE 0.033 0.003 PHE G 316 TYR 0.016 0.002 TYR I 57 ARG 0.005 0.001 ARG J 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 215 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 26 LYS cc_start: 0.8359 (mmmt) cc_final: 0.7582 (tppt) REVERT: I 37 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7745 (tp30) REVERT: I 42 LYS cc_start: 0.8896 (ttpp) cc_final: 0.8363 (ttmm) REVERT: I 54 MET cc_start: 0.8275 (mmm) cc_final: 0.7506 (mmm) REVERT: J 42 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8111 (mtmt) REVERT: J 196 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7326 (mt) REVERT: K 66 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7302 (tt0) REVERT: K 76 MET cc_start: 0.7948 (mmt) cc_final: 0.7577 (tpp) REVERT: K 93 ASP cc_start: 0.7700 (t0) cc_final: 0.7488 (t0) REVERT: K 212 ARG cc_start: 0.7904 (ttt-90) cc_final: 0.6894 (ttm110) REVERT: M 39 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7776 (tm-30) REVERT: M 42 MET cc_start: 0.7839 (mmm) cc_final: 0.7515 (tpt) REVERT: M 50 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7978 (tp30) REVERT: N 88 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7564 (pp30) REVERT: a 209 PRO cc_start: 0.8947 (Cg_endo) cc_final: 0.8712 (Cg_exo) REVERT: a 243 SER cc_start: 0.7752 (OUTLIER) cc_final: 0.7523 (t) REVERT: a 295 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8336 (tp) outliers start: 60 outliers final: 38 residues processed: 251 average time/residue: 0.2412 time to fit residues: 86.0213 Evaluate side-chains 249 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 207 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 201 ASP Chi-restraints excluded: chain J residue 208 MET Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain a residue 58 CYS Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain a residue 130 PHE Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 218 SER Chi-restraints excluded: chain a residue 243 SER Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 256 GLU Chi-restraints excluded: chain a residue 261 VAL Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 341 THR Chi-restraints excluded: chain a residue 348 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 40.0000 chunk 79 optimal weight: 10.0000 chunk 112 optimal weight: 50.0000 chunk 167 optimal weight: 0.9980 chunk 177 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 206 GLN N 53 GLN a 14 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12423 Z= 0.204 Angle : 0.491 8.551 16900 Z= 0.266 Chirality : 0.035 0.157 2065 Planarity : 0.003 0.026 2306 Dihedral : 4.280 48.528 1983 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.25 % Rotamer: Outliers : 6.83 % Allowed : 27.80 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 3.37 (0.20), residues: 1856 helix: 3.05 (0.13), residues: 1429 sheet: 0.40 (0.62), residues: 76 loop : -1.10 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 293 HIS 0.001 0.000 HIS a 343 PHE 0.040 0.002 PHE G 316 TYR 0.014 0.001 TYR I 57 ARG 0.006 0.000 ARG G 309 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 216 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 61 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.7905 (tp) REVERT: I 26 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7332 (tppt) REVERT: I 37 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7733 (tp30) REVERT: I 42 LYS cc_start: 0.8906 (ttpp) cc_final: 0.8356 (ttmm) REVERT: I 54 MET cc_start: 0.8437 (mmm) cc_final: 0.7711 (mmm) REVERT: I 62 LYS cc_start: 0.9228 (tppt) cc_final: 0.8882 (ttpt) REVERT: J 42 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8135 (ttmm) REVERT: K 66 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7222 (tt0) REVERT: K 76 MET cc_start: 0.7853 (mmt) cc_final: 0.7446 (tpp) REVERT: K 93 ASP cc_start: 0.7685 (t0) cc_final: 0.7466 (t0) REVERT: K 212 ARG cc_start: 0.7816 (ttt-90) cc_final: 0.6661 (ttm170) REVERT: M 39 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7779 (tm-30) REVERT: M 42 MET cc_start: 0.7819 (mmm) cc_final: 0.7234 (tpt) REVERT: M 50 GLU cc_start: 0.8238 (mt-10) cc_final: 0.8003 (tp30) REVERT: M 96 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6072 (tt) REVERT: N 88 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7580 (pp30) REVERT: a 209 PRO cc_start: 0.8941 (Cg_endo) cc_final: 0.8647 (Cg_exo) REVERT: a 338 ARG cc_start: 0.8114 (tpp80) cc_final: 0.7706 (mmm-85) outliers start: 56 outliers final: 41 residues processed: 246 average time/residue: 0.2357 time to fit residues: 82.4457 Evaluate side-chains 243 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 199 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 208 MET Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 208 MET Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain a residue 58 CYS Chi-restraints excluded: chain a residue 94 MET Chi-restraints excluded: chain a residue 96 ASP Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain a residue 130 PHE Chi-restraints excluded: chain a residue 138 PHE Chi-restraints excluded: chain a residue 170 PHE Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 218 SER Chi-restraints excluded: chain a residue 232 ARG Chi-restraints excluded: chain a residue 243 SER Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 256 GLU Chi-restraints excluded: chain a residue 268 LEU Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 351 ILE Chi-restraints excluded: chain a residue 352 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 53 GLN O 91 ASN a 14 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12423 Z= 0.220 Angle : 0.506 8.946 16900 Z= 0.273 Chirality : 0.036 0.149 2065 Planarity : 0.003 0.027 2306 Dihedral : 4.100 39.826 1979 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.07 % Favored : 96.88 % Rotamer: Outliers : 6.95 % Allowed : 28.66 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 3.35 (0.20), residues: 1856 helix: 3.04 (0.13), residues: 1430 sheet: 0.70 (0.65), residues: 66 loop : -1.19 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 324 HIS 0.001 0.000 HIS a 343 PHE 0.029 0.002 PHE G 316 TYR 0.019 0.001 TYR I 56 ARG 0.006 0.001 ARG K 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 203 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 61 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7836 (tp) REVERT: G 317 GLN cc_start: 0.7676 (pm20) cc_final: 0.7232 (pt0) REVERT: I 26 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7360 (tppt) REVERT: I 37 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7714 (tp30) REVERT: I 42 LYS cc_start: 0.8879 (ttpp) cc_final: 0.8294 (ttmm) REVERT: I 54 MET cc_start: 0.8425 (mmm) cc_final: 0.7483 (mmm) REVERT: I 62 LYS cc_start: 0.9189 (tppt) cc_final: 0.8873 (ttpt) REVERT: J 42 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8172 (ttmm) REVERT: J 115 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7842 (tt) REVERT: K 66 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7227 (tt0) REVERT: K 76 MET cc_start: 0.7910 (mmt) cc_final: 0.7463 (tpp) REVERT: K 212 ARG cc_start: 0.7819 (ttt-90) cc_final: 0.6593 (ttm170) REVERT: M 39 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7775 (tm-30) REVERT: M 42 MET cc_start: 0.7785 (mmm) cc_final: 0.7529 (tpt) REVERT: M 50 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7988 (tp30) REVERT: M 96 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6102 (tt) REVERT: N 88 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7542 (pp30) REVERT: a 196 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6942 (t80) REVERT: a 209 PRO cc_start: 0.8994 (Cg_endo) cc_final: 0.8744 (Cg_exo) REVERT: a 295 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8346 (tp) outliers start: 57 outliers final: 43 residues processed: 233 average time/residue: 0.2282 time to fit residues: 76.4631 Evaluate side-chains 244 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 195 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 208 MET Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain a residue 94 MET Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 111 ILE Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain a residue 130 PHE Chi-restraints excluded: chain a residue 138 PHE Chi-restraints excluded: chain a residue 170 PHE Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 196 PHE Chi-restraints excluded: chain a residue 218 SER Chi-restraints excluded: chain a residue 232 ARG Chi-restraints excluded: chain a residue 243 SER Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 256 GLU Chi-restraints excluded: chain a residue 268 LEU Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain a residue 320 ILE Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 341 THR Chi-restraints excluded: chain a residue 348 VAL Chi-restraints excluded: chain a residue 351 ILE Chi-restraints excluded: chain a residue 352 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.8980 chunk 160 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 178 optimal weight: 0.6980 chunk 147 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 53 GLN ** a 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12423 Z= 0.152 Angle : 0.471 9.126 16900 Z= 0.255 Chirality : 0.034 0.160 2065 Planarity : 0.003 0.035 2306 Dihedral : 3.771 35.154 1978 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.21 % Favored : 97.74 % Rotamer: Outliers : 5.49 % Allowed : 29.39 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 3.73 (0.20), residues: 1856 helix: 3.30 (0.13), residues: 1437 sheet: 0.13 (0.61), residues: 79 loop : -0.93 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 282 HIS 0.001 0.000 HIS G 296 PHE 0.025 0.001 PHE G 316 TYR 0.015 0.001 TYR I 56 ARG 0.008 0.001 ARG M 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 220 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 317 GLN cc_start: 0.7650 (pm20) cc_final: 0.7297 (pt0) REVERT: I 26 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7327 (tppt) REVERT: I 42 LYS cc_start: 0.8850 (ttpp) cc_final: 0.8191 (ttmm) REVERT: I 54 MET cc_start: 0.8419 (mmm) cc_final: 0.7532 (mmm) REVERT: I 62 LYS cc_start: 0.9156 (tppt) cc_final: 0.8899 (ttpt) REVERT: J 101 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7783 (tpp80) REVERT: J 115 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7811 (tt) REVERT: K 76 MET cc_start: 0.7754 (mmt) cc_final: 0.7361 (tpp) REVERT: K 212 ARG cc_start: 0.7679 (ttt-90) cc_final: 0.6428 (ttm170) REVERT: M 39 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7738 (tm-30) REVERT: M 42 MET cc_start: 0.7745 (mmm) cc_final: 0.7223 (tpt) REVERT: M 50 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7974 (tp30) REVERT: M 96 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6052 (tt) REVERT: N 88 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7477 (pp30) REVERT: a 28 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7834 (mm-30) REVERT: a 196 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6842 (t80) REVERT: a 209 PRO cc_start: 0.8969 (Cg_endo) cc_final: 0.8736 (Cg_exo) REVERT: a 232 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.8052 (ttm170) outliers start: 45 outliers final: 32 residues processed: 241 average time/residue: 0.2351 time to fit residues: 80.9828 Evaluate side-chains 237 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 201 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain J residue 208 MET Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain a residue 94 MET Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 130 PHE Chi-restraints excluded: chain a residue 170 PHE Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 196 PHE Chi-restraints excluded: chain a residue 232 ARG Chi-restraints excluded: chain a residue 243 SER Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 256 GLU Chi-restraints excluded: chain a residue 261 VAL Chi-restraints excluded: chain a residue 268 LEU Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 341 THR Chi-restraints excluded: chain a residue 348 VAL Chi-restraints excluded: chain a residue 351 ILE Chi-restraints excluded: chain a residue 352 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 101 optimal weight: 30.0000 chunk 130 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 chunk 177 optimal weight: 1.9990 chunk 110 optimal weight: 30.0000 chunk 108 optimal weight: 30.0000 chunk 81 optimal weight: 8.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 14 HIS J 113 GLN a 48 GLN a 278 HIS ** a 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 12423 Z= 0.572 Angle : 0.843 13.687 16900 Z= 0.446 Chirality : 0.046 0.177 2065 Planarity : 0.005 0.054 2306 Dihedral : 5.244 57.990 1978 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.09 % Favored : 95.85 % Rotamer: Outliers : 9.39 % Allowed : 29.02 % Favored : 61.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.19), residues: 1856 helix: 1.94 (0.13), residues: 1432 sheet: 0.08 (0.60), residues: 72 loop : -1.59 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP a 188 HIS 0.004 0.001 HIS G 296 PHE 0.029 0.004 PHE G 316 TYR 0.021 0.002 TYR a 23 ARG 0.011 0.001 ARG G 301 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 203 time to evaluate : 1.500 Fit side-chains revert: symmetry clash REVERT: G 312 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7155 (mt) REVERT: G 317 GLN cc_start: 0.7896 (pm20) cc_final: 0.7482 (pt0) REVERT: I 37 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7783 (tp30) REVERT: I 54 MET cc_start: 0.8459 (mmm) cc_final: 0.8128 (mmm) REVERT: I 194 ASN cc_start: 0.6551 (OUTLIER) cc_final: 0.6169 (t0) REVERT: I 208 MET cc_start: 0.8283 (tpp) cc_final: 0.8048 (tpp) REVERT: J 115 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8266 (tt) REVERT: J 196 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7677 (mt) REVERT: K 76 MET cc_start: 0.8136 (mmt) cc_final: 0.7695 (tpp) REVERT: K 203 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8495 (tp) REVERT: K 212 ARG cc_start: 0.8011 (ttt-90) cc_final: 0.6762 (ttm170) REVERT: M 42 MET cc_start: 0.7973 (mmm) cc_final: 0.7713 (tpt) REVERT: M 96 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6053 (tt) REVERT: a 12 LEU cc_start: 0.8573 (tp) cc_final: 0.8232 (mp) REVERT: a 28 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7928 (mm-30) REVERT: a 94 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.8039 (tmt) REVERT: a 295 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8453 (tp) REVERT: a 352 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7679 (pp) outliers start: 77 outliers final: 48 residues processed: 255 average time/residue: 0.2214 time to fit residues: 81.7359 Evaluate side-chains 240 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 183 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 286 ASN Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 312 LEU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 194 ASN Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 196 LEU Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain J residue 208 MET Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain a residue 58 CYS Chi-restraints excluded: chain a residue 94 MET Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 111 ILE Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 126 THR Chi-restraints excluded: chain a residue 130 PHE Chi-restraints excluded: chain a residue 138 PHE Chi-restraints excluded: chain a residue 170 PHE Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 218 SER Chi-restraints excluded: chain a residue 222 ILE Chi-restraints excluded: chain a residue 232 ARG Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 256 GLU Chi-restraints excluded: chain a residue 261 VAL Chi-restraints excluded: chain a residue 268 LEU Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 341 THR Chi-restraints excluded: chain a residue 348 VAL Chi-restraints excluded: chain a residue 352 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 50.0000 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 20.0000 chunk 112 optimal weight: 50.0000 chunk 120 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 16 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 161 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 106 ASN ** a 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12423 Z= 0.251 Angle : 0.574 9.350 16900 Z= 0.307 Chirality : 0.037 0.171 2065 Planarity : 0.003 0.033 2306 Dihedral : 4.529 55.430 1978 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.20 % Rotamer: Outliers : 6.59 % Allowed : 32.68 % Favored : 60.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 2.75 (0.20), residues: 1856 helix: 2.62 (0.13), residues: 1434 sheet: -0.23 (0.59), residues: 76 loop : -1.33 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 107 HIS 0.001 0.000 HIS a 343 PHE 0.022 0.002 PHE J 216 TYR 0.014 0.001 TYR G 310 ARG 0.006 0.001 ARG G 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 207 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 306 SER cc_start: 0.5921 (p) cc_final: 0.5304 (p) REVERT: G 308 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8440 (tt) REVERT: G 312 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7085 (mt) REVERT: I 26 LYS cc_start: 0.8246 (mmmt) cc_final: 0.7279 (tppt) REVERT: I 37 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7738 (tp30) REVERT: I 42 LYS cc_start: 0.8808 (ttpp) cc_final: 0.8399 (ttmm) REVERT: I 62 LYS cc_start: 0.9161 (tppt) cc_final: 0.8869 (ttmt) REVERT: I 208 MET cc_start: 0.8117 (tpp) cc_final: 0.7872 (tpp) REVERT: J 16 MET cc_start: 0.7368 (mmm) cc_final: 0.7145 (mmt) REVERT: J 115 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8183 (tt) REVERT: J 207 MET cc_start: 0.6660 (OUTLIER) cc_final: 0.6408 (ttm) REVERT: K 76 MET cc_start: 0.7917 (mmt) cc_final: 0.7513 (tpp) REVERT: K 203 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8323 (tp) REVERT: K 212 ARG cc_start: 0.7847 (ttt-90) cc_final: 0.6496 (ttm170) REVERT: M 42 MET cc_start: 0.7928 (mmm) cc_final: 0.7600 (tpt) REVERT: M 50 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7954 (tp30) REVERT: M 96 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6053 (tt) REVERT: a 28 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7868 (mm-30) REVERT: a 94 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7953 (tmt) REVERT: a 209 PRO cc_start: 0.9096 (Cg_endo) cc_final: 0.8790 (Cg_exo) REVERT: a 293 TRP cc_start: 0.8132 (m-10) cc_final: 0.7589 (m-10) REVERT: a 316 GLN cc_start: 0.7910 (tp-100) cc_final: 0.7653 (tp40) outliers start: 54 outliers final: 41 residues processed: 241 average time/residue: 0.2390 time to fit residues: 82.4824 Evaluate side-chains 245 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 197 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 286 ASN Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 312 LEU Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain J residue 208 MET Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 203 ILE Chi-restraints excluded: chain K residue 208 MET Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain a residue 94 MET Chi-restraints excluded: chain a residue 96 ASP Chi-restraints excluded: chain a residue 111 ILE Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 130 PHE Chi-restraints excluded: chain a residue 138 PHE Chi-restraints excluded: chain a residue 170 PHE Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 232 ARG Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 256 GLU Chi-restraints excluded: chain a residue 261 VAL Chi-restraints excluded: chain a residue 268 LEU Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 341 THR Chi-restraints excluded: chain a residue 348 VAL Chi-restraints excluded: chain a residue 352 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 165 optimal weight: 0.0770 chunk 99 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 149 optimal weight: 20.0000 chunk 156 optimal weight: 0.6980 chunk 164 optimal weight: 8.9990 chunk 108 optimal weight: 40.0000 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 106 ASN ** a 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12423 Z= 0.160 Angle : 0.517 9.338 16900 Z= 0.276 Chirality : 0.034 0.169 2065 Planarity : 0.003 0.027 2306 Dihedral : 3.982 51.579 1978 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.86 % Favored : 97.09 % Rotamer: Outliers : 4.76 % Allowed : 34.39 % Favored : 60.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 3.40 (0.20), residues: 1856 helix: 3.12 (0.13), residues: 1440 sheet: 0.05 (0.56), residues: 85 loop : -1.40 (0.36), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 107 HIS 0.002 0.000 HIS G 296 PHE 0.018 0.002 PHE J 216 TYR 0.014 0.001 TYR I 56 ARG 0.006 0.001 ARG G 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 221 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 26 LYS cc_start: 0.8083 (mmmt) cc_final: 0.7187 (tppt) REVERT: I 42 LYS cc_start: 0.8710 (ttpp) cc_final: 0.8329 (ttmm) REVERT: I 62 LYS cc_start: 0.9105 (tppt) cc_final: 0.8864 (ttmt) REVERT: J 115 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8120 (tt) REVERT: J 215 LEU cc_start: 0.8222 (tp) cc_final: 0.7592 (tp) REVERT: K 76 MET cc_start: 0.7765 (mmt) cc_final: 0.7368 (tpp) REVERT: K 212 ARG cc_start: 0.7587 (ttt-90) cc_final: 0.5567 (mtt180) REVERT: M 42 MET cc_start: 0.7870 (mmm) cc_final: 0.7598 (tpt) REVERT: M 50 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7932 (tp30) REVERT: M 96 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.5974 (tt) REVERT: a 295 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8418 (tp) outliers start: 39 outliers final: 29 residues processed: 245 average time/residue: 0.2216 time to fit residues: 78.6689 Evaluate side-chains 235 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 203 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain a residue 58 CYS Chi-restraints excluded: chain a residue 96 ASP Chi-restraints excluded: chain a residue 111 ILE Chi-restraints excluded: chain a residue 130 PHE Chi-restraints excluded: chain a residue 138 PHE Chi-restraints excluded: chain a residue 170 PHE Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 256 GLU Chi-restraints excluded: chain a residue 261 VAL Chi-restraints excluded: chain a residue 268 LEU Chi-restraints excluded: chain a residue 295 ILE Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 341 THR Chi-restraints excluded: chain a residue 348 VAL Chi-restraints excluded: chain a residue 352 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 121 optimal weight: 20.0000 chunk 183 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 15 optimal weight: 40.0000 chunk 112 optimal weight: 50.0000 chunk 89 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 317 GLN J 100 GLN ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12423 Z= 0.235 Angle : 0.588 12.914 16900 Z= 0.307 Chirality : 0.036 0.177 2065 Planarity : 0.003 0.042 2306 Dihedral : 4.062 55.275 1976 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.18 % Favored : 96.77 % Rotamer: Outliers : 3.90 % Allowed : 35.98 % Favored : 60.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 3.38 (0.20), residues: 1856 helix: 3.11 (0.13), residues: 1434 sheet: -0.13 (0.56), residues: 87 loop : -1.29 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 188 HIS 0.002 0.001 HIS J 14 PHE 0.027 0.002 PHE G 316 TYR 0.016 0.002 TYR G 310 ARG 0.010 0.001 ARG G 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 201 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: G 306 SER cc_start: 0.5840 (p) cc_final: 0.5610 (p) REVERT: I 26 LYS cc_start: 0.8139 (mmmt) cc_final: 0.7388 (tppt) REVERT: I 42 LYS cc_start: 0.8754 (ttpp) cc_final: 0.8337 (ttmm) REVERT: I 62 LYS cc_start: 0.9117 (tppt) cc_final: 0.8881 (ttmt) REVERT: I 208 MET cc_start: 0.8058 (tpp) cc_final: 0.7835 (mmp) REVERT: J 115 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8100 (tt) REVERT: J 215 LEU cc_start: 0.8161 (tp) cc_final: 0.7840 (tp) REVERT: K 76 MET cc_start: 0.7921 (mmt) cc_final: 0.7534 (tpp) REVERT: K 212 ARG cc_start: 0.7683 (ttt-90) cc_final: 0.5529 (mtt180) REVERT: M 42 MET cc_start: 0.7910 (mmm) cc_final: 0.7647 (tpt) REVERT: M 50 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7934 (tp30) REVERT: M 96 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.5952 (tt) REVERT: M 102 MET cc_start: 0.6502 (ttt) cc_final: 0.6274 (ttt) REVERT: a 94 MET cc_start: 0.8152 (ttt) cc_final: 0.7517 (tmm) REVERT: a 316 GLN cc_start: 0.7857 (tp-100) cc_final: 0.7643 (tp40) outliers start: 32 outliers final: 29 residues processed: 223 average time/residue: 0.2231 time to fit residues: 72.3968 Evaluate side-chains 231 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 200 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 40 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain J residue 115 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 62 LYS Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 103 VAL Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain a residue 96 ASP Chi-restraints excluded: chain a residue 108 LEU Chi-restraints excluded: chain a residue 111 ILE Chi-restraints excluded: chain a residue 138 PHE Chi-restraints excluded: chain a residue 170 PHE Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 250 THR Chi-restraints excluded: chain a residue 256 GLU Chi-restraints excluded: chain a residue 261 VAL Chi-restraints excluded: chain a residue 268 LEU Chi-restraints excluded: chain a residue 315 THR Chi-restraints excluded: chain a residue 332 SER Chi-restraints excluded: chain a residue 341 THR Chi-restraints excluded: chain a residue 348 VAL Chi-restraints excluded: chain a residue 352 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 18 optimal weight: 40.0000 chunk 26 optimal weight: 30.0000 chunk 128 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.171840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.148561 restraints weight = 29592.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.148615 restraints weight = 20600.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.148883 restraints weight = 17764.976| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12423 Z= 0.273 Angle : 0.602 10.378 16900 Z= 0.319 Chirality : 0.037 0.170 2065 Planarity : 0.003 0.040 2306 Dihedral : 4.209 58.799 1976 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.50 % Favored : 96.44 % Rotamer: Outliers : 5.00 % Allowed : 35.24 % Favored : 59.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 3.18 (0.20), residues: 1856 helix: 2.97 (0.13), residues: 1435 sheet: -0.21 (0.56), residues: 87 loop : -1.40 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 188 HIS 0.001 0.000 HIS J 14 PHE 0.048 0.002 PHE I 18 TYR 0.016 0.002 TYR G 310 ARG 0.009 0.001 ARG G 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2377.17 seconds wall clock time: 48 minutes 7.19 seconds (2887.19 seconds total)