Starting phenix.real_space_refine on Sun Apr 7 11:38:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qno_4598/04_2024/6qno_4598_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qno_4598/04_2024/6qno_4598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qno_4598/04_2024/6qno_4598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qno_4598/04_2024/6qno_4598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qno_4598/04_2024/6qno_4598_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qno_4598/04_2024/6qno_4598_neut_updated.pdb" } resolution = 4.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 6647 2.51 5 N 1718 2.21 5 O 1986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 180": "NH1" <-> "NH2" Residue "H TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 69": "NH1" <-> "NH2" Residue "R TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 314": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10429 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1711 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 209} Chain breaks: 2 Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2392 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 306} Chain: "G" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 293 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "L" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1679 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 205} Chain: "H" Number of atoms: 1660 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 1654 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 206} Conformer: "B" Number of residues, atoms: 221, 1654 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 206} bond proxies already assigned to first conformer: 1692 Chain: "R" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2646 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 19, 'TRANS': 314} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N SER L 42 " occ=0.94 ... (4 atoms not shown) pdb=" OG SER L 42 " occ=0.94 residue: pdb=" N SER H 176 " occ=0.54 ... (7 atoms not shown) pdb=" OG BSER H 176 " occ=0.34 residue: pdb=" N GLN R 64 " occ=0.50 ... (7 atoms not shown) pdb=" NE2 GLN R 64 " occ=0.50 residue: pdb=" N TRP R 161 " occ=0.50 ... (12 atoms not shown) pdb=" CH2 TRP R 161 " occ=0.50 residue: pdb=" N PHE R 313 " occ=0.50 ... (9 atoms not shown) pdb=" CZ PHE R 313 " occ=0.50 Time building chain proxies: 6.83, per 1000 atoms: 0.65 Number of scatterers: 10429 At special positions: 0 Unit cell: (90.47, 117.86, 156.04, 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 78 16.00 O 1986 8.00 N 1718 7.00 C 6647 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 113 " distance=2.04 Simple disulfide: pdb=" SG CYS L 159 " - pdb=" SG CYS L 219 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.04 Simple disulfide: pdb=" SG CYS H 167 " - pdb=" SG CYS H 222 " distance=2.04 Simple disulfide: pdb=" SG CYS R 2 " - pdb=" SG CYS R 282 " distance=2.03 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 187 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN R 15 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.34 Conformation dependent library (CDL) restraints added in 2.2 seconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2474 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 18 sheets defined 25.4% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 14 through 26 removed outlier: 3.734A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.513A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.817A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 297 through 308 Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.685A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'G' and resid 33 through 47 removed outlier: 4.790A pdb=" N GLU G 46 " --> pdb=" O ASP G 42 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ARG G 47 " --> pdb=" O TYR G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 61 No H-bonds generated for 'chain 'G' and resid 59 through 61' Processing helix chain 'L' and resid 147 through 152 Processing helix chain 'L' and resid 175 through 177 No H-bonds generated for 'chain 'L' and resid 175 through 177' Processing helix chain 'L' and resid 209 through 212 No H-bonds generated for 'chain 'L' and resid 209 through 212' Processing helix chain 'H' and resid 48 through 50 No H-bonds generated for 'chain 'H' and resid 48 through 50' Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'H' and resid 107 through 109 No H-bonds generated for 'chain 'H' and resid 107 through 109' Processing helix chain 'R' and resid 34 through 64 Proline residue: R 53 - end of helix Processing helix chain 'R' and resid 66 through 68 No H-bonds generated for 'chain 'R' and resid 66 through 68' Processing helix chain 'R' and resid 74 through 100 removed outlier: 4.192A pdb=" N PHE R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N THR R 92 " --> pdb=" O PHE R 88 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR R 93 " --> pdb=" O GLY R 89 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR R 94 " --> pdb=" O GLY R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 140 Processing helix chain 'R' and resid 150 through 168 removed outlier: 3.729A pdb=" N CYS R 167 " --> pdb=" O MET R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 172 No H-bonds generated for 'chain 'R' and resid 170 through 172' Processing helix chain 'R' and resid 200 through 236 removed outlier: 4.309A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) Proline residue: R 215 - end of helix Processing helix chain 'R' and resid 241 through 277 Proline residue: R 267 - end of helix Processing helix chain 'R' and resid 285 through 305 removed outlier: 3.923A pdb=" N ILE R 290 " --> pdb=" O ILE R 286 " (cutoff:3.500A) Proline residue: R 291 - end of helix Proline residue: R 303 - end of helix Processing helix chain 'R' and resid 311 through 318 removed outlier: 5.528A pdb=" N CYS R 316 " --> pdb=" O GLN R 312 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N MET R 317 " --> pdb=" O PHE R 313 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL R 318 " --> pdb=" O ARG R 314 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 221 through 224 removed outlier: 3.859A pdb=" N PHE A 267 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.725A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 105 removed outlier: 4.085A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 180 Processing sheet with id= E, first strand: chain 'B' and resid 220 through 222 removed outlier: 4.103A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 262 through 264 removed outlier: 3.714A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA B 240 " --> pdb=" O PHE B 235 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 277 removed outlier: 7.062A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.568A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 24 through 26 Processing sheet with id= J, first strand: chain 'L' and resid 58 through 63 Processing sheet with id= K, first strand: chain 'L' and resid 139 through 143 removed outlier: 6.125A pdb=" N TYR L 198 " --> pdb=" O ASN L 163 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 170 through 175 Processing sheet with id= M, first strand: chain 'H' and resid 22 through 26 removed outlier: 3.911A pdb=" N GLY H 35 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ARG H 37 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N THR H 103 " --> pdb=" O ARG H 37 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU H 39 " --> pdb=" O GLN H 101 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLN H 101 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N CYS H 41 " --> pdb=" O PHE H 99 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE H 99 " --> pdb=" O CYS H 41 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ALA H 43 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR H 97 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.074A pdb=" N ARG H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N TRP H 66 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 147 through 151 removed outlier: 6.457A pdb=" N TYR H 202 " --> pdb=" O GLY H 171 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 177 through 181 Processing sheet with id= Q, first strand: chain 'H' and resid 196 through 198 Processing sheet with id= R, first strand: chain 'R' and resid 178 through 181 removed outlier: 4.261A pdb=" N SER R 186 " --> pdb=" O GLU R 181 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1145 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: 2.86 Time building geometry restraints manager: 5.70 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: 3215 1.34 - 1.46: 2756 1.46 - 1.59: 4591 1.59 - 1.71: 5 1.71 - 1.83: 113 Bond restraints: 10680 Sorted by residual: bond pdb=" C6 RET R 401 " pdb=" C7 RET R 401 " ideal model delta sigma weight residual 1.459 1.657 -0.198 2.00e-02 2.50e+03 9.80e+01 bond pdb=" C8 RET R 401 " pdb=" C9 RET R 401 " ideal model delta sigma weight residual 1.450 1.593 -0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" C10 RET R 401 " pdb=" C11 RET R 401 " ideal model delta sigma weight residual 1.433 1.548 -0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C14 RET R 401 " pdb=" C15 RET R 401 " ideal model delta sigma weight residual 1.448 1.536 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C12 RET R 401 " pdb=" C13 RET R 401 " ideal model delta sigma weight residual 1.446 1.534 -0.088 2.00e-02 2.50e+03 1.94e+01 ... (remaining 10675 not shown) Histogram of bond angle deviations from ideal: 96.71 - 104.18: 164 104.18 - 111.65: 4652 111.65 - 119.12: 3998 119.12 - 126.60: 5520 126.60 - 134.07: 164 Bond angle restraints: 14498 Sorted by residual: angle pdb=" N PRO R 170 " pdb=" CA PRO R 170 " pdb=" C PRO R 170 " ideal model delta sigma weight residual 110.70 117.34 -6.64 1.22e+00 6.72e-01 2.96e+01 angle pdb=" C GLN A 204 " pdb=" N ARG A 205 " pdb=" CA ARG A 205 " ideal model delta sigma weight residual 121.54 130.63 -9.09 1.91e+00 2.74e-01 2.26e+01 angle pdb=" C LYS R 311 " pdb=" N GLN R 312 " pdb=" CA GLN R 312 " ideal model delta sigma weight residual 120.38 126.94 -6.56 1.46e+00 4.69e-01 2.02e+01 angle pdb=" CA GLU A 43 " pdb=" CB GLU A 43 " pdb=" CG GLU A 43 " ideal model delta sigma weight residual 114.10 122.49 -8.39 2.00e+00 2.50e-01 1.76e+01 angle pdb=" CA TYR R 301 " pdb=" CB TYR R 301 " pdb=" CG TYR R 301 " ideal model delta sigma weight residual 113.90 121.38 -7.48 1.80e+00 3.09e-01 1.73e+01 ... (remaining 14493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.88: 5828 15.88 - 31.76: 406 31.76 - 47.64: 73 47.64 - 63.52: 12 63.52 - 79.39: 8 Dihedral angle restraints: 6327 sinusoidal: 2470 harmonic: 3857 Sorted by residual: dihedral pdb=" CA PHE H 173 " pdb=" C PHE H 173 " pdb=" N PRO H 174 " pdb=" CA PRO H 174 " ideal model delta harmonic sigma weight residual 180.00 125.94 54.06 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" CA TRP R 175 " pdb=" C TRP R 175 " pdb=" N SER R 176 " pdb=" CA SER R 176 " ideal model delta harmonic sigma weight residual 180.00 -127.18 -52.82 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA PRO R 327 " pdb=" C PRO R 327 " pdb=" N LEU R 328 " pdb=" CA LEU R 328 " ideal model delta harmonic sigma weight residual 180.00 130.79 49.21 0 5.00e+00 4.00e-02 9.69e+01 ... (remaining 6324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1206 0.071 - 0.142: 357 0.142 - 0.212: 53 0.212 - 0.283: 4 0.283 - 0.354: 4 Chirality restraints: 1624 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN R 15 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CB ILE H 119 " pdb=" CA ILE H 119 " pdb=" CG1 ILE H 119 " pdb=" CG2 ILE H 119 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CG LEU H 237 " pdb=" CB LEU H 237 " pdb=" CD1 LEU H 237 " pdb=" CD2 LEU H 237 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 1621 not shown) Planarity restraints: 1842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 297 " 0.041 2.00e-02 2.50e+03 2.60e-02 1.69e+01 pdb=" CG TRP B 297 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP B 297 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 297 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 297 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 297 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 297 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 297 " 0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 297 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 297 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 130 " 0.008 2.00e-02 2.50e+03 1.97e-02 9.67e+00 pdb=" CG TRP H 130 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP H 130 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP H 130 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 130 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP H 130 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP H 130 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 130 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 130 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP H 130 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 163 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.69e+00 pdb=" C ASP B 163 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP B 163 " -0.019 2.00e-02 2.50e+03 pdb=" N THR B 164 " -0.017 2.00e-02 2.50e+03 ... (remaining 1839 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1927 2.76 - 3.30: 10054 3.30 - 3.83: 17912 3.83 - 4.37: 19755 4.37 - 4.90: 32976 Nonbonded interactions: 82624 Sorted by model distance: nonbonded pdb=" O PHE R 273 " pdb=" OG1 THR R 277 " model vdw 2.227 2.440 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR B 173 " pdb=" OE1 GLN B 175 " model vdw 2.243 2.440 nonbonded pdb=" OG SER L 90 " pdb=" O THR L 97 " model vdw 2.245 2.440 nonbonded pdb=" O VAL R 157 " pdb=" OG1 THR R 160 " model vdw 2.251 2.440 ... (remaining 82619 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.34 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 0.000 Extract box with map and model: 8.310 Check model and map are aligned: 0.160 Set scattering table: 0.120 Process input model: 33.960 Find NCS groups from input model: 0.320 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.010 0.198 10680 Z= 0.683 Angle : 1.248 12.112 14498 Z= 0.683 Chirality : 0.066 0.354 1624 Planarity : 0.008 0.069 1841 Dihedral : 11.761 79.395 3835 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 1.65 % Allowed : 3.83 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.16 % 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: -3.96 (0.19), residues: 1318 helix: -2.37 (0.21), residues: 341 sheet: -1.91 (0.26), residues: 322 loop : -3.18 (0.21), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.006 TRP B 297 HIS 0.027 0.005 HIS H 54 PHE 0.042 0.005 PHE A 215 TYR 0.041 0.004 TYR R 257 ARG 0.010 0.002 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 208 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8725 (m-40) cc_final: 0.7306 (t0) REVERT: A 304 GLN cc_start: 0.7462 (tt0) cc_final: 0.7188 (tm-30) REVERT: B 76 ASP cc_start: 0.8235 (p0) cc_final: 0.7855 (t0) REVERT: B 187 VAL cc_start: 0.7742 (t) cc_final: 0.7526 (t) REVERT: B 313 ASN cc_start: 0.8473 (t0) cc_final: 0.8100 (t0) REVERT: G 36 CYS cc_start: 0.8316 (m) cc_final: 0.7326 (m) REVERT: G 39 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8751 (mt-10) REVERT: L 34 THR cc_start: 0.8661 (m) cc_final: 0.8190 (p) REVERT: L 37 GLU cc_start: 0.8563 (mt-10) cc_final: 0.7986 (mt-10) REVERT: H 172 TYR cc_start: 0.7838 (p90) cc_final: 0.7177 (p90) REVERT: R 39 MET cc_start: 0.7449 (mmp) cc_final: 0.7203 (mmm) REVERT: R 69 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.7608 (ptp-170) REVERT: R 207 MET cc_start: 0.9121 (mmm) cc_final: 0.8705 (tpp) REVERT: R 253 MET cc_start: 0.9315 (mmm) cc_final: 0.8899 (mmm) REVERT: R 308 MET cc_start: 0.8799 (mtp) cc_final: 0.8479 (mtp) outliers start: 16 outliers final: 6 residues processed: 222 average time/residue: 0.2829 time to fit residues: 83.2425 Evaluate side-chains 119 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 204 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 62 HIS B 91 HIS B 176 GLN B 183 HIS B 295 ASN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 163 ASN L 235 ASN ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 HIS R 73 ASN R 100 HIS ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 199 ASN R 302 ASN R 312 GLN ** R 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10680 Z= 0.215 Angle : 0.738 9.027 14498 Z= 0.391 Chirality : 0.046 0.215 1624 Planarity : 0.005 0.052 1841 Dihedral : 7.837 67.762 1488 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.35 % Allowed : 4.35 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.16 % 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: -2.99 (0.21), residues: 1318 helix: -1.06 (0.25), residues: 341 sheet: -1.65 (0.26), residues: 321 loop : -2.69 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 82 HIS 0.007 0.001 HIS R 65 PHE 0.017 0.002 PHE L 96 TYR 0.029 0.002 TYR R 301 ARG 0.007 0.001 ARG L 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8740 (m-40) cc_final: 0.7528 (t0) REVERT: A 24 ARG cc_start: 0.8565 (ppt170) cc_final: 0.8306 (ttp80) REVERT: B 58 ILE cc_start: 0.8823 (mt) cc_final: 0.8240 (pt) REVERT: B 76 ASP cc_start: 0.8092 (p0) cc_final: 0.7857 (t0) REVERT: B 80 ILE cc_start: 0.8445 (mt) cc_final: 0.8236 (mt) REVERT: B 91 HIS cc_start: 0.6850 (m90) cc_final: 0.6548 (m170) REVERT: B 111 TYR cc_start: 0.8157 (m-10) cc_final: 0.7662 (m-10) REVERT: B 217 MET cc_start: 0.6978 (mpp) cc_final: 0.6756 (mpp) REVERT: B 313 ASN cc_start: 0.8410 (t0) cc_final: 0.8154 (t0) REVERT: G 36 CYS cc_start: 0.8175 (m) cc_final: 0.6620 (m) REVERT: G 39 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8703 (mt-10) REVERT: L 34 THR cc_start: 0.8764 (m) cc_final: 0.8318 (p) REVERT: L 37 GLU cc_start: 0.8617 (mt-10) cc_final: 0.7931 (mt-10) REVERT: L 172 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8263 (mtmm) REVERT: L 190 ASP cc_start: 0.8061 (p0) cc_final: 0.7810 (p0) REVERT: H 22 GLN cc_start: 0.7721 (mp10) cc_final: 0.7421 (mp10) REVERT: H 172 TYR cc_start: 0.7833 (p90) cc_final: 0.7223 (p90) REVERT: R 69 ARG cc_start: 0.8128 (mtm-85) cc_final: 0.7406 (mpt-90) REVERT: R 183 MET cc_start: 0.8862 (mtm) cc_final: 0.8462 (mmm) REVERT: R 207 MET cc_start: 0.9017 (mmm) cc_final: 0.8527 (tpp) REVERT: R 253 MET cc_start: 0.9300 (mmm) cc_final: 0.8990 (mmt) REVERT: R 302 ASN cc_start: 0.8790 (m110) cc_final: 0.8195 (m110) REVERT: R 305 ILE cc_start: 0.9322 (pt) cc_final: 0.9020 (tt) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.2921 time to fit residues: 74.0541 Evaluate side-chains 125 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 99 optimal weight: 0.4980 chunk 81 optimal weight: 0.0870 chunk 32 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 128 optimal weight: 0.2980 chunk 106 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 95 optimal weight: 7.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 312 GLN ** R 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10680 Z= 0.171 Angle : 0.674 8.220 14498 Z= 0.353 Chirality : 0.045 0.212 1624 Planarity : 0.005 0.049 1841 Dihedral : 6.951 69.353 1488 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.43 % Allowed : 3.30 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.16 % 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: -2.47 (0.22), residues: 1318 helix: -0.54 (0.27), residues: 347 sheet: -1.27 (0.27), residues: 304 loop : -2.46 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 175 HIS 0.006 0.001 HIS R 65 PHE 0.041 0.002 PHE R 85 TYR 0.017 0.002 TYR A 287 ARG 0.007 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 186 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8772 (m-40) cc_final: 0.7301 (t0) REVERT: A 24 ARG cc_start: 0.8592 (ppt170) cc_final: 0.8262 (ttp80) REVERT: B 111 TYR cc_start: 0.8141 (m-10) cc_final: 0.7667 (m-10) REVERT: B 313 ASN cc_start: 0.8403 (t0) cc_final: 0.8059 (t0) REVERT: B 325 MET cc_start: 0.7678 (tmm) cc_final: 0.7132 (tmm) REVERT: G 36 CYS cc_start: 0.7941 (m) cc_final: 0.7154 (m) REVERT: L 22 ILE cc_start: 0.9113 (mt) cc_final: 0.8875 (pt) REVERT: L 34 THR cc_start: 0.8845 (m) cc_final: 0.8340 (p) REVERT: L 37 GLU cc_start: 0.8588 (mt-10) cc_final: 0.7838 (mt-10) REVERT: L 123 PHE cc_start: 0.7327 (m-10) cc_final: 0.7099 (m-10) REVERT: L 172 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8162 (mtmm) REVERT: L 190 ASP cc_start: 0.8055 (p0) cc_final: 0.7824 (p0) REVERT: H 22 GLN cc_start: 0.7762 (mp10) cc_final: 0.7414 (mp10) REVERT: H 172 TYR cc_start: 0.7726 (p90) cc_final: 0.7158 (p90) REVERT: R 69 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7480 (mtt90) REVERT: R 183 MET cc_start: 0.8765 (mtm) cc_final: 0.8444 (mmm) REVERT: R 189 ILE cc_start: 0.8502 (pt) cc_final: 0.8202 (mp) REVERT: R 207 MET cc_start: 0.8931 (mmm) cc_final: 0.8720 (tpp) REVERT: R 253 MET cc_start: 0.9186 (mmm) cc_final: 0.8833 (mmt) REVERT: R 265 TRP cc_start: 0.8236 (m100) cc_final: 0.8012 (m100) REVERT: R 305 ILE cc_start: 0.9308 (pt) cc_final: 0.8947 (tt) outliers start: 2 outliers final: 1 residues processed: 187 average time/residue: 0.2601 time to fit residues: 67.5048 Evaluate side-chains 138 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 61 optimal weight: 0.0030 chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 80 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 311 HIS ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 HIS ** R 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10680 Z= 0.153 Angle : 0.648 8.349 14498 Z= 0.338 Chirality : 0.044 0.220 1624 Planarity : 0.004 0.046 1841 Dihedral : 6.461 71.489 1488 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.26 % Allowed : 2.09 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.16 % 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: -2.09 (0.22), residues: 1318 helix: -0.12 (0.27), residues: 345 sheet: -1.14 (0.27), residues: 316 loop : -2.25 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 175 HIS 0.005 0.001 HIS H 226 PHE 0.019 0.002 PHE R 273 TYR 0.013 0.001 TYR R 178 ARG 0.005 0.000 ARG R 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8774 (m-40) cc_final: 0.7331 (t0) REVERT: A 188 HIS cc_start: 0.8243 (m-70) cc_final: 0.8011 (m-70) REVERT: B 111 TYR cc_start: 0.8065 (m-10) cc_final: 0.7801 (m-10) REVERT: B 253 PHE cc_start: 0.6184 (m-80) cc_final: 0.5897 (m-10) REVERT: B 262 MET cc_start: 0.7096 (mmm) cc_final: 0.6868 (mmm) REVERT: B 313 ASN cc_start: 0.8369 (t0) cc_final: 0.7970 (t0) REVERT: B 325 MET cc_start: 0.7716 (tmm) cc_final: 0.7166 (ppp) REVERT: L 190 ASP cc_start: 0.8060 (p0) cc_final: 0.7825 (p0) REVERT: H 112 MET cc_start: 0.8172 (tpt) cc_final: 0.7764 (tpp) REVERT: H 172 TYR cc_start: 0.7618 (p90) cc_final: 0.7068 (p90) REVERT: H 198 GLN cc_start: 0.8647 (tp40) cc_final: 0.8167 (tp40) REVERT: R 69 ARG cc_start: 0.8132 (mtm-85) cc_final: 0.7447 (mtt90) REVERT: R 86 MET cc_start: 0.8091 (mmm) cc_final: 0.7856 (mmp) REVERT: R 183 MET cc_start: 0.8716 (mtm) cc_final: 0.8320 (pmm) REVERT: R 189 ILE cc_start: 0.8538 (pt) cc_final: 0.8275 (mp) REVERT: R 223 TYR cc_start: 0.9042 (m-80) cc_final: 0.8826 (m-80) REVERT: R 253 MET cc_start: 0.9156 (mmm) cc_final: 0.8774 (mmt) REVERT: R 305 ILE cc_start: 0.9279 (pt) cc_final: 0.8870 (tt) REVERT: R 309 MET cc_start: 0.8423 (mmm) cc_final: 0.8004 (mmm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2728 time to fit residues: 67.2997 Evaluate side-chains 128 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN B 91 HIS ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 115 GLN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10680 Z= 0.245 Angle : 0.672 8.590 14498 Z= 0.351 Chirality : 0.044 0.210 1624 Planarity : 0.004 0.044 1841 Dihedral : 6.535 70.399 1488 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 0.35 % Allowed : 2.00 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % 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: -2.05 (0.22), residues: 1318 helix: 0.04 (0.28), residues: 343 sheet: -1.09 (0.27), residues: 321 loop : -2.31 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 126 HIS 0.007 0.001 HIS B 54 PHE 0.016 0.002 PHE B 151 TYR 0.013 0.002 TYR B 264 ARG 0.007 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8766 (m-40) cc_final: 0.7363 (t0) REVERT: A 24 ARG cc_start: 0.9048 (ttp-170) cc_final: 0.8586 (ttp80) REVERT: A 188 HIS cc_start: 0.8253 (m-70) cc_final: 0.8038 (m-70) REVERT: B 75 GLN cc_start: 0.8763 (mm110) cc_final: 0.8397 (mm-40) REVERT: B 111 TYR cc_start: 0.8147 (m-10) cc_final: 0.7519 (m-10) REVERT: B 313 ASN cc_start: 0.8479 (t0) cc_final: 0.8166 (t0) REVERT: B 325 MET cc_start: 0.7904 (tmm) cc_final: 0.7304 (ppp) REVERT: G 35 LYS cc_start: 0.7206 (ptmt) cc_final: 0.6766 (ptmt) REVERT: G 38 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8285 (pt0) REVERT: L 190 ASP cc_start: 0.8130 (p0) cc_final: 0.7902 (p0) REVERT: H 172 TYR cc_start: 0.7719 (p90) cc_final: 0.7145 (p90) REVERT: R 69 ARG cc_start: 0.8177 (mtm-85) cc_final: 0.7487 (mtt90) REVERT: R 86 MET cc_start: 0.8167 (mmm) cc_final: 0.7917 (mmp) REVERT: R 183 MET cc_start: 0.8859 (mtm) cc_final: 0.8609 (mmm) REVERT: R 189 ILE cc_start: 0.8685 (pt) cc_final: 0.8381 (mp) REVERT: R 253 MET cc_start: 0.9171 (mmm) cc_final: 0.8738 (mmt) REVERT: R 296 LYS cc_start: 0.8578 (mmpt) cc_final: 0.8338 (mtmm) REVERT: R 305 ILE cc_start: 0.9333 (pt) cc_final: 0.9044 (tt) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.2568 time to fit residues: 54.0982 Evaluate side-chains 116 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.3980 chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 chunk 126 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 115 GLN ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10680 Z= 0.215 Angle : 0.669 9.817 14498 Z= 0.349 Chirality : 0.044 0.241 1624 Planarity : 0.004 0.044 1841 Dihedral : 6.338 70.703 1488 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.35 % Allowed : 1.74 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % 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: -1.94 (0.22), residues: 1318 helix: 0.12 (0.27), residues: 342 sheet: -1.04 (0.27), residues: 321 loop : -2.23 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 126 HIS 0.006 0.001 HIS B 54 PHE 0.013 0.002 PHE B 151 TYR 0.014 0.001 TYR R 301 ARG 0.007 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8704 (m-40) cc_final: 0.7327 (t0) REVERT: A 24 ARG cc_start: 0.9050 (ttp-170) cc_final: 0.8374 (ttp80) REVERT: A 186 GLU cc_start: 0.8452 (pt0) cc_final: 0.7898 (mp0) REVERT: A 188 HIS cc_start: 0.8438 (m-70) cc_final: 0.7731 (m-70) REVERT: B 75 GLN cc_start: 0.8919 (mm110) cc_final: 0.8402 (mm-40) REVERT: B 253 PHE cc_start: 0.6529 (m-80) cc_final: 0.6305 (m-80) REVERT: B 313 ASN cc_start: 0.8388 (t0) cc_final: 0.8006 (t0) REVERT: G 35 LYS cc_start: 0.7174 (ptmt) cc_final: 0.6603 (ptmt) REVERT: G 38 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8220 (pt0) REVERT: L 76 MET cc_start: 0.8461 (tmm) cc_final: 0.8260 (tmm) REVERT: L 190 ASP cc_start: 0.8153 (p0) cc_final: 0.7884 (p0) REVERT: H 172 TYR cc_start: 0.7633 (p90) cc_final: 0.7060 (p90) REVERT: R 69 ARG cc_start: 0.8133 (mtm-85) cc_final: 0.7467 (mtt90) REVERT: R 86 MET cc_start: 0.8192 (mmm) cc_final: 0.7957 (mmp) REVERT: R 183 MET cc_start: 0.8797 (mtm) cc_final: 0.8529 (mmm) REVERT: R 189 ILE cc_start: 0.8749 (pt) cc_final: 0.8458 (mp) REVERT: R 253 MET cc_start: 0.9165 (mmm) cc_final: 0.8711 (mmt) REVERT: R 305 ILE cc_start: 0.9431 (pt) cc_final: 0.9084 (tt) outliers start: 1 outliers final: 1 residues processed: 150 average time/residue: 0.2578 time to fit residues: 52.9359 Evaluate side-chains 114 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10680 Z= 0.197 Angle : 0.660 8.152 14498 Z= 0.344 Chirality : 0.044 0.308 1624 Planarity : 0.004 0.044 1841 Dihedral : 6.245 71.289 1488 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.26 % Allowed : 0.96 % Favored : 98.78 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % 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: -1.83 (0.23), residues: 1318 helix: 0.10 (0.28), residues: 344 sheet: -0.90 (0.28), residues: 318 loop : -2.13 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 82 HIS 0.005 0.001 HIS R 65 PHE 0.029 0.002 PHE L 123 TYR 0.013 0.001 TYR R 301 ARG 0.007 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8679 (m-40) cc_final: 0.7322 (t0) REVERT: A 24 ARG cc_start: 0.9035 (ttp-170) cc_final: 0.8378 (ttp80) REVERT: A 186 GLU cc_start: 0.8479 (pt0) cc_final: 0.7907 (mp0) REVERT: A 188 HIS cc_start: 0.8333 (m-70) cc_final: 0.7666 (m-70) REVERT: A 305 CYS cc_start: 0.7644 (m) cc_final: 0.7334 (t) REVERT: B 75 GLN cc_start: 0.8965 (mm110) cc_final: 0.8211 (mm-40) REVERT: B 313 ASN cc_start: 0.8393 (t0) cc_final: 0.8076 (t0) REVERT: B 325 MET cc_start: 0.8600 (ttp) cc_final: 0.7287 (ppp) REVERT: G 38 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8202 (pt0) REVERT: L 190 ASP cc_start: 0.8142 (p0) cc_final: 0.7875 (p0) REVERT: H 172 TYR cc_start: 0.7611 (p90) cc_final: 0.7072 (p90) REVERT: R 69 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7444 (mtt90) REVERT: R 86 MET cc_start: 0.8148 (mmm) cc_final: 0.7934 (mmp) REVERT: R 183 MET cc_start: 0.8798 (mtm) cc_final: 0.8450 (pmm) REVERT: R 189 ILE cc_start: 0.8684 (pt) cc_final: 0.8432 (mp) REVERT: R 253 MET cc_start: 0.9171 (mmm) cc_final: 0.8671 (mmt) REVERT: R 305 ILE cc_start: 0.9416 (pt) cc_final: 0.9063 (tt) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2596 time to fit residues: 54.6189 Evaluate side-chains 110 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 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 241 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10680 Z= 0.238 Angle : 0.716 12.780 14498 Z= 0.367 Chirality : 0.045 0.362 1624 Planarity : 0.004 0.049 1841 Dihedral : 6.229 70.616 1488 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 0.35 % Allowed : 1.13 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % 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: -1.87 (0.22), residues: 1318 helix: 0.16 (0.28), residues: 338 sheet: -1.06 (0.27), residues: 325 loop : -2.12 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 175 HIS 0.006 0.001 HIS B 54 PHE 0.030 0.002 PHE G 64 TYR 0.012 0.002 TYR R 301 ARG 0.010 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8695 (m-40) cc_final: 0.7336 (t0) REVERT: A 24 ARG cc_start: 0.9038 (ttp-170) cc_final: 0.8546 (ttp80) REVERT: A 186 GLU cc_start: 0.8527 (pt0) cc_final: 0.7957 (mp0) REVERT: A 188 HIS cc_start: 0.8351 (m-70) cc_final: 0.7648 (m-70) REVERT: A 242 ARG cc_start: 0.5556 (mtt-85) cc_final: 0.4923 (mmt180) REVERT: B 253 PHE cc_start: 0.6573 (m-80) cc_final: 0.6369 (m-80) REVERT: B 262 MET cc_start: 0.7297 (mmm) cc_final: 0.7005 (mmm) REVERT: B 313 ASN cc_start: 0.8485 (t0) cc_final: 0.8216 (t0) REVERT: B 325 MET cc_start: 0.8713 (ttp) cc_final: 0.8063 (ppp) REVERT: G 38 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8184 (pt0) REVERT: L 190 ASP cc_start: 0.8176 (p0) cc_final: 0.7908 (p0) REVERT: H 172 TYR cc_start: 0.7574 (p90) cc_final: 0.7029 (p90) REVERT: R 69 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7469 (mtt90) REVERT: R 86 MET cc_start: 0.8124 (mmm) cc_final: 0.7922 (mmp) REVERT: R 155 MET cc_start: 0.9318 (ppp) cc_final: 0.9113 (ppp) REVERT: R 183 MET cc_start: 0.8829 (mtm) cc_final: 0.8448 (pmm) REVERT: R 189 ILE cc_start: 0.8724 (pt) cc_final: 0.8502 (mp) REVERT: R 253 MET cc_start: 0.9189 (mmm) cc_final: 0.8673 (mmt) REVERT: R 305 ILE cc_start: 0.9398 (pt) cc_final: 0.9021 (tt) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.2703 time to fit residues: 54.6312 Evaluate side-chains 110 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 77 optimal weight: 0.0040 chunk 124 optimal weight: 1.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10680 Z= 0.179 Angle : 0.645 7.690 14498 Z= 0.335 Chirality : 0.044 0.200 1624 Planarity : 0.004 0.051 1841 Dihedral : 6.290 70.778 1488 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.35 % Allowed : 0.43 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.08 % 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: -1.74 (0.23), residues: 1318 helix: 0.27 (0.28), residues: 338 sheet: -1.00 (0.27), residues: 336 loop : -2.03 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 126 HIS 0.005 0.001 HIS R 65 PHE 0.038 0.002 PHE R 159 TYR 0.011 0.001 TYR H 121 ARG 0.006 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8673 (m-40) cc_final: 0.7331 (t0) REVERT: A 24 ARG cc_start: 0.9017 (ttp-170) cc_final: 0.8523 (ttp80) REVERT: A 186 GLU cc_start: 0.8481 (pt0) cc_final: 0.7883 (mp0) REVERT: A 188 HIS cc_start: 0.8310 (m-70) cc_final: 0.7614 (m-70) REVERT: A 242 ARG cc_start: 0.5590 (mtt-85) cc_final: 0.4960 (mmt180) REVERT: A 305 CYS cc_start: 0.7681 (m) cc_final: 0.7375 (t) REVERT: B 75 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8556 (mm-40) REVERT: B 262 MET cc_start: 0.6960 (mmm) cc_final: 0.6642 (mmm) REVERT: B 313 ASN cc_start: 0.8434 (t0) cc_final: 0.8133 (t0) REVERT: B 325 MET cc_start: 0.8764 (ttp) cc_final: 0.8347 (ppp) REVERT: G 64 PHE cc_start: 0.7576 (m-10) cc_final: 0.7341 (m-10) REVERT: L 190 ASP cc_start: 0.8143 (p0) cc_final: 0.7870 (p0) REVERT: H 172 TYR cc_start: 0.7486 (p90) cc_final: 0.6998 (p90) REVERT: R 69 ARG cc_start: 0.8125 (mtm-85) cc_final: 0.7444 (mtt90) REVERT: R 86 MET cc_start: 0.8124 (mmm) cc_final: 0.7761 (mmp) REVERT: R 155 MET cc_start: 0.9327 (ppp) cc_final: 0.9109 (ppp) REVERT: R 253 MET cc_start: 0.9170 (mmm) cc_final: 0.8608 (mmt) outliers start: 1 outliers final: 1 residues processed: 150 average time/residue: 0.2417 time to fit residues: 50.4156 Evaluate side-chains 108 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 86 optimal weight: 0.0020 chunk 130 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 110 optimal weight: 0.9980 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 HIS ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10680 Z= 0.175 Angle : 0.654 14.352 14498 Z= 0.337 Chirality : 0.044 0.242 1624 Planarity : 0.004 0.046 1841 Dihedral : 6.077 70.136 1488 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.26 % Allowed : 0.17 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 1.85 % 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: -1.65 (0.23), residues: 1318 helix: 0.41 (0.28), residues: 338 sheet: -1.03 (0.28), residues: 319 loop : -1.96 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 175 HIS 0.006 0.001 HIS B 54 PHE 0.037 0.002 PHE R 159 TYR 0.015 0.001 TYR R 178 ARG 0.006 0.001 ARG A 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.8661 (m-40) cc_final: 0.7360 (t0) REVERT: A 24 ARG cc_start: 0.9008 (ttp-170) cc_final: 0.8448 (ttp80) REVERT: A 188 HIS cc_start: 0.8304 (m-70) cc_final: 0.7834 (m90) REVERT: B 75 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8643 (mm-40) REVERT: B 313 ASN cc_start: 0.8437 (t0) cc_final: 0.8132 (t0) REVERT: B 325 MET cc_start: 0.8737 (ttp) cc_final: 0.8371 (ppp) REVERT: L 102 ARG cc_start: 0.9061 (ptp90) cc_final: 0.8647 (ptp90) REVERT: L 123 PHE cc_start: 0.6383 (m-80) cc_final: 0.6064 (m-80) REVERT: L 190 ASP cc_start: 0.8115 (p0) cc_final: 0.7844 (p0) REVERT: H 172 TYR cc_start: 0.7512 (p90) cc_final: 0.7028 (p90) REVERT: R 69 ARG cc_start: 0.8126 (mtm-85) cc_final: 0.7410 (mtt90) REVERT: R 86 MET cc_start: 0.8105 (mmm) cc_final: 0.7765 (mmp) REVERT: R 155 MET cc_start: 0.9317 (ppp) cc_final: 0.9083 (ppp) REVERT: R 253 MET cc_start: 0.9173 (mmm) cc_final: 0.8594 (mmt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2437 time to fit residues: 51.8218 Evaluate side-chains 110 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 91 optimal weight: 0.0030 chunk 5 optimal weight: 0.6980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 326 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 = 0.3840 r_free = 0.3840 target = 0.081083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.065812 restraints weight = 65058.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.065935 restraints weight = 36923.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.066523 restraints weight = 30543.671| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10680 Z= 0.159 Angle : 0.637 12.259 14498 Z= 0.330 Chirality : 0.044 0.205 1624 Planarity : 0.004 0.061 1841 Dihedral : 5.940 70.312 1488 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.26 % Allowed : 0.17 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -1.55 (0.23), residues: 1318 helix: 0.54 (0.28), residues: 332 sheet: -0.94 (0.27), residues: 332 loop : -1.94 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 175 HIS 0.005 0.001 HIS H 226 PHE 0.036 0.001 PHE R 159 TYR 0.012 0.001 TYR B 264 ARG 0.008 0.000 ARG A 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2443.74 seconds wall clock time: 45 minutes 44.76 seconds (2744.76 seconds total)