Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 5 19:00:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qno_4598/07_2023/6qno_4598_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qno_4598/07_2023/6qno_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_4598/07_2023/6qno_4598.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qno_4598/07_2023/6qno_4598.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qno_4598/07_2023/6qno_4598_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qno_4598/07_2023/6qno_4598_neut_updated.pdb" } resolution = 4.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-5013/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 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: 6.31, per 1000 atoms: 0.61 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: 4.36 Conformation dependent library (CDL) restraints added in 1.7 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: 0.93 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: 2.92 Time building geometry restraints manager: 4.66 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: 5790 15.88 - 31.76: 405 31.76 - 47.64: 70 47.64 - 63.52: 12 63.52 - 79.39: 8 Dihedral angle restraints: 6285 sinusoidal: 2428 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 6282 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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.720 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 30.470 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.020 ------------------------------------------------------------------------------- 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 : 11.753 79.395 3793 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 % 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 *********************** 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 : 1.334 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 outliers start: 16 outliers final: 6 residues processed: 222 average time/residue: 0.2791 time to fit residues: 82.3407 Evaluate side-chains 111 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 1.282 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1043 time to fit residues: 2.6965 ------------------------------------------------------------------------------- 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: 0.6980 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 33 optimal weight: 0.3980 chunk 66 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** ** A 304 GLN ** 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 Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 10680 Z= 0.213 Angle : 0.740 8.786 14498 Z= 0.393 Chirality : 0.046 0.206 1624 Planarity : 0.005 0.053 1841 Dihedral : 7.718 67.790 1446 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer Outliers : 0.52 % 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: -3.02 (0.21), residues: 1318 helix: -1.06 (0.25), residues: 340 sheet: -1.65 (0.26), residues: 314 loop : -2.73 (0.21), residues: 664 *********************** 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 189 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 186 time to evaluate : 1.295 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 outliers start: 3 outliers final: 2 residues processed: 189 average time/residue: 0.2721 time to fit residues: 69.3107 Evaluate side-chains 117 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0970 time to fit residues: 2.0734 ------------------------------------------------------------------------------- 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: 7.9990 chunk 36 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 119 optimal weight: 0.0000 chunk 128 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 95 optimal weight: 0.3980 overall best weight: 1.8790 ------------------------------------------------------------------------------- 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** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** 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 195 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 10680 Z= 0.237 Angle : 0.716 9.663 14498 Z= 0.377 Chirality : 0.045 0.200 1624 Planarity : 0.005 0.045 1841 Dihedral : 7.091 68.382 1446 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer Outliers : 0.35 % 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: -2.60 (0.21), residues: 1318 helix: -0.65 (0.26), residues: 343 sheet: -1.31 (0.28), residues: 294 loop : -2.54 (0.22), residues: 681 *********************** 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 163 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 1.303 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 outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.2477 time to fit residues: 55.7478 Evaluate side-chains 113 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6008 ------------------------------------------------------------------------------- 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: 6.9990 chunk 89 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 HIS ** 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: 0.7484 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10680 Z= 0.183 Angle : 0.667 8.308 14498 Z= 0.348 Chirality : 0.045 0.245 1624 Planarity : 0.004 0.043 1841 Dihedral : 6.653 70.438 1446 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer Outliers : 0.26 % 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: -2.31 (0.22), residues: 1318 helix: -0.34 (0.27), residues: 346 sheet: -1.21 (0.27), residues: 309 loop : -2.39 (0.23), residues: 663 *********************** 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 170 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.162 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 outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2673 time to fit residues: 61.7816 Evaluate side-chains 115 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5654 ------------------------------------------------------------------------------- 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: 7.9990 chunk 71 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 52 optimal weight: 0.2980 chunk 108 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 116 HIS ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 244 GLN ** R 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.118 10680 Z= 0.397 Angle : 0.811 10.914 14498 Z= 0.426 Chirality : 0.048 0.204 1624 Planarity : 0.005 0.057 1841 Dihedral : 7.077 68.496 1446 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 25.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer Outliers : 0.43 % 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: -2.53 (0.21), residues: 1318 helix: -0.53 (0.26), residues: 339 sheet: -1.43 (0.26), residues: 316 loop : -2.46 (0.23), residues: 663 *********************** 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 135 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 1.374 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 outliers start: 2 outliers final: 0 residues processed: 135 average time/residue: 0.2657 time to fit residues: 49.4608 Evaluate side-chains 101 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.249 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6132 ------------------------------------------------------------------------------- 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: 1.9990 chunk 114 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 HIS ** 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: 0.7638 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 10680 Z= 0.308 Angle : 0.734 9.750 14498 Z= 0.387 Chirality : 0.046 0.271 1624 Planarity : 0.005 0.051 1841 Dihedral : 6.849 69.687 1446 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 22.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer Outliers : 0.35 % 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: -2.43 (0.21), residues: 1318 helix: -0.36 (0.26), residues: 335 sheet: -1.49 (0.26), residues: 321 loop : -2.37 (0.23), residues: 662 *********************** 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 140 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.298 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 outliers start: 1 outliers final: 1 residues processed: 140 average time/residue: 0.2506 time to fit residues: 49.1487 Evaluate side-chains 107 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0976 time to fit residues: 1.8151 ------------------------------------------------------------------------------- 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: 4.9990 chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 HIS ** 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: 0.7655 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 10680 Z= 0.309 Angle : 0.740 9.988 14498 Z= 0.388 Chirality : 0.046 0.209 1624 Planarity : 0.005 0.054 1841 Dihedral : 6.770 68.614 1446 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Rotamer Outliers : 0.26 % 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: -2.41 (0.22), residues: 1318 helix: -0.34 (0.27), residues: 332 sheet: -1.49 (0.26), residues: 317 loop : -2.34 (0.23), residues: 669 *********************** 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 135 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.242 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 outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2492 time to fit residues: 47.0766 Evaluate side-chains 102 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4960 ------------------------------------------------------------------------------- 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: 4.9990 chunk 50 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 114 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** 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: 0.7529 moved from start: 0.4313 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= 0.175 Angle : 0.664 9.589 14498 Z= 0.344 Chirality : 0.045 0.185 1624 Planarity : 0.004 0.052 1841 Dihedral : 6.341 69.858 1446 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer Outliers : 0.26 % 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: -1.97 (0.22), residues: 1318 helix: 0.21 (0.28), residues: 329 sheet: -1.29 (0.27), residues: 310 loop : -2.12 (0.23), residues: 679 *********************** 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 161 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.206 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 outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2592 time to fit residues: 57.8888 Evaluate side-chains 115 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.329 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7523 ------------------------------------------------------------------------------- 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: 1.9990 chunk 110 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 0.0050 chunk 36 optimal weight: 6.9990 chunk 106 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 77 optimal weight: 0.0370 chunk 124 optimal weight: 1.9990 overall best weight: 0.5072 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** 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: 0.7496 moved from start: 0.4536 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= 0.182 Angle : 0.709 12.361 14498 Z= 0.359 Chirality : 0.046 0.431 1624 Planarity : 0.004 0.046 1841 Dihedral : 6.208 69.339 1446 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer Outliers : 0.26 % 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: -1.88 (0.22), residues: 1318 helix: 0.27 (0.28), residues: 328 sheet: -1.16 (0.28), residues: 309 loop : -2.10 (0.23), residues: 681 *********************** 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: 0 poor density : 150 time to evaluate : 1.341 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 outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2664 time to fit residues: 54.6552 Evaluate side-chains 109 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6115 ------------------------------------------------------------------------------- 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: 3.9990 chunk 59 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** 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: 0.7573 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 10680 Z= 0.241 Angle : 0.769 23.521 14498 Z= 0.383 Chirality : 0.046 0.487 1624 Planarity : 0.004 0.047 1841 Dihedral : 6.188 67.884 1446 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.08 % 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: -1.89 (0.22), residues: 1318 helix: 0.25 (0.28), residues: 328 sheet: -1.19 (0.27), residues: 320 loop : -2.09 (0.23), residues: 670 ********************** 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 137 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.212 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 outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2554 time to fit residues: 48.6654 Evaluate side-chains 110 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.261 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6258 ------------------------------------------------------------------------------- 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: 4.9990 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 0.1980 chunk 104 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 HIS ** R 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.078864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.064169 restraints weight = 69218.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.064216 restraints weight = 41968.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.064665 restraints weight = 35397.455| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 10680 Z= 0.252 Angle : 0.715 13.732 14498 Z= 0.370 Chirality : 0.045 0.236 1624 Planarity : 0.004 0.047 1841 Dihedral : 6.627 84.953 1446 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer Outliers : 0.26 % 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: -1.92 (0.22), residues: 1318 helix: 0.19 (0.28), residues: 327 sheet: -1.18 (0.28), residues: 310 loop : -2.10 (0.23), residues: 681 =============================================================================== Job complete usr+sys time: 2259.20 seconds wall clock time: 42 minutes 6.85 seconds (2526.85 seconds total)