Starting phenix.real_space_refine on Mon Mar 11 17:00:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6g_31479/03_2024/7f6g_31479_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6g_31479/03_2024/7f6g_31479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6g_31479/03_2024/7f6g_31479.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6g_31479/03_2024/7f6g_31479.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6g_31479/03_2024/7f6g_31479_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6g_31479/03_2024/7f6g_31479_updated.pdb" } resolution = 2.9 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 52 5.16 5 C 5631 2.51 5 N 1451 2.21 5 O 1563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8697 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2520 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 12, 'TRANS': 297} Chain: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 72 Classifications: {'peptide': 8} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2890 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 337} Chain: "C" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 182 Unusual residues: {'CLR': 6, 'NAG': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.13, per 1000 atoms: 0.59 Number of scatterers: 8697 At special positions: 0 Unit cell: (101.4, 100.386, 130.806, 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 52 16.00 O 1563 8.00 N 1451 7.00 C 5631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 180 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 176 " Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.6 seconds 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2022 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 9 sheets defined 44.8% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 27 through 55 Proline residue: A 32 - end of helix removed outlier: 3.571A pdb=" N LEU A 48 " --> pdb=" O PHE A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 79 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 98 through 131 removed outlier: 3.618A pdb=" N ALA A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 142 through 166 Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 190 through 201 removed outlier: 3.807A pdb=" N LEU A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 196 " --> pdb=" O PRO A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 229 Processing helix chain 'A' and resid 235 through 268 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 274 through 291 removed outlier: 4.048A pdb=" N ILE A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 293 through 301 Proline residue: A 299 - end of helix Processing helix chain 'A' and resid 307 through 319 Processing helix chain 'B' and resid 13 through 38 removed outlier: 3.806A pdb=" N GLU B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 62 removed outlier: 3.526A pdb=" N MET B 59 " --> pdb=" O PHE B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 96 removed outlier: 3.797A pdb=" N GLY B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE B 75 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP B 95 " --> pdb=" O ILE B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 115 removed outlier: 4.276A pdb=" N ALA B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 137 removed outlier: 3.547A pdb=" N ALA B 131 " --> pdb=" O PRO B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 146 Processing helix chain 'B' and resid 157 through 162 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 213 through 220 removed outlier: 5.083A pdb=" N HIS B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N CYS B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N PHE B 220 " --> pdb=" O TRP B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 247 through 260 Processing helix chain 'B' and resid 262 through 266 removed outlier: 4.415A pdb=" N ASN B 266 " --> pdb=" O TRP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 282 Processing helix chain 'B' and resid 302 through 316 removed outlier: 3.592A pdb=" N ARG B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 316 " --> pdb=" O MET B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 355 Processing helix chain 'C' and resid 4 through 24 Processing helix chain 'C' and resid 30 through 36 removed outlier: 5.099A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing sheet with id= A, first strand: chain 'A' and resid 12 through 14 removed outlier: 4.179A pdb=" N LYS A 12 " --> pdb=" O VAL A 169 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.604A pdb=" N VAL B 269 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N HIS B 327 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU B 271 " --> pdb=" O HIS B 327 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER B 225 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 229 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE B 200 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU B 42 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ARG B 202 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 44 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL B 204 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLY B 46 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 190 " --> pdb=" O ASP B 205 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.841A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.860A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.641A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.787A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 250 through 254 Processing sheet with id= H, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.562A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.657A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1146 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: 2.39 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2431 1.34 - 1.46: 1762 1.46 - 1.58: 4626 1.58 - 1.70: 0 1.70 - 1.83: 77 Bond restraints: 8896 Sorted by residual: bond pdb=" C10 CLR A 405 " pdb=" C5 CLR A 405 " ideal model delta sigma weight residual 1.519 1.386 0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C4 CLR A 405 " pdb=" C5 CLR A 405 " ideal model delta sigma weight residual 1.506 1.380 0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C10 CLR A 404 " pdb=" C5 CLR A 404 " ideal model delta sigma weight residual 1.519 1.403 0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" C10 CLR A 402 " pdb=" C5 CLR A 402 " ideal model delta sigma weight residual 1.519 1.404 0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C10 CLR A 406 " pdb=" C5 CLR A 406 " ideal model delta sigma weight residual 1.519 1.404 0.115 2.00e-02 2.50e+03 3.31e+01 ... (remaining 8891 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.45: 163 105.45 - 112.72: 4741 112.72 - 119.99: 3363 119.99 - 127.26: 3738 127.26 - 134.52: 81 Bond angle restraints: 12086 Sorted by residual: angle pdb=" CA GLY A 97 " pdb=" C GLY A 97 " pdb=" O GLY A 97 " ideal model delta sigma weight residual 122.23 118.06 4.17 6.90e-01 2.10e+00 3.65e+01 angle pdb=" C LYS A 232 " pdb=" CA LYS A 232 " pdb=" CB LYS A 232 " ideal model delta sigma weight residual 110.71 115.64 -4.93 9.40e-01 1.13e+00 2.75e+01 angle pdb=" CA LYS A 232 " pdb=" C LYS A 232 " pdb=" N PRO A 233 " ideal model delta sigma weight residual 118.16 121.29 -3.13 7.00e-01 2.04e+00 2.00e+01 angle pdb=" CA VAL B 184 " pdb=" C VAL B 184 " pdb=" N PRO B 185 " ideal model delta sigma weight residual 119.30 122.77 -3.47 8.10e-01 1.52e+00 1.83e+01 angle pdb=" N LEU B 358 " pdb=" CA LEU B 358 " pdb=" C LEU B 358 " ideal model delta sigma weight residual 112.45 106.63 5.82 1.39e+00 5.18e-01 1.75e+01 ... (remaining 12081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.68: 5309 23.68 - 47.35: 276 47.35 - 71.03: 32 71.03 - 94.71: 8 94.71 - 118.39: 2 Dihedral angle restraints: 5627 sinusoidal: 2505 harmonic: 3122 Sorted by residual: dihedral pdb=" CA SER C 227 " pdb=" C SER C 227 " pdb=" N ASP C 228 " pdb=" CA ASP C 228 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" C10 CLR A 405 " pdb=" C1 CLR A 405 " pdb=" C2 CLR A 405 " pdb=" C3 CLR A 405 " ideal model delta sinusoidal sigma weight residual -56.83 61.56 -118.39 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" CA PHE C 222 " pdb=" C PHE C 222 " pdb=" N THR C 223 " pdb=" CA THR C 223 " ideal model delta harmonic sigma weight residual -180.00 -160.25 -19.75 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 5624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1190 0.097 - 0.195: 157 0.195 - 0.292: 18 0.292 - 0.389: 9 0.389 - 0.487: 11 Chirality restraints: 1385 Sorted by residual: chirality pdb=" C14 CLR A 402 " pdb=" C13 CLR A 402 " pdb=" C15 CLR A 402 " pdb=" C8 CLR A 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.80 0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" C14 CLR A 405 " pdb=" C13 CLR A 405 " pdb=" C15 CLR A 405 " pdb=" C8 CLR A 405 " both_signs ideal model delta sigma weight residual False -2.32 -2.79 0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" C14 CLR A 403 " pdb=" C13 CLR A 403 " pdb=" C15 CLR A 403 " pdb=" C8 CLR A 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.78 0.47 2.00e-01 2.50e+01 5.41e+00 ... (remaining 1382 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 161 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO A 162 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 162 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 162 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 62 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.02e+00 pdb=" C ILE B 62 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE B 62 " 0.013 2.00e-02 2.50e+03 pdb=" N HIS B 63 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 223 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C THR C 223 " -0.033 2.00e-02 2.50e+03 pdb=" O THR C 223 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY C 224 " 0.011 2.00e-02 2.50e+03 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 566 2.74 - 3.28: 8655 3.28 - 3.82: 13661 3.82 - 4.36: 17915 4.36 - 4.90: 29534 Nonbonded interactions: 70331 Sorted by model distance: nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.197 2.440 nonbonded pdb=" O SER C 67 " pdb=" OG SER C 67 " model vdw 2.284 2.440 nonbonded pdb=" NZ LYS A 102 " pdb=" O ILE A 164 " model vdw 2.335 2.520 nonbonded pdb=" OD2 ASP B 236 " pdb=" NZ LYS B 282 " model vdw 2.342 2.520 nonbonded pdb=" O ASP A 278 " pdb=" OG1 THR A 282 " model vdw 2.355 2.440 ... (remaining 70326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.180 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: 3.320 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.110 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 : 0.009 0.133 8896 Z= 0.572 Angle : 0.976 8.160 12086 Z= 0.646 Chirality : 0.080 0.487 1385 Planarity : 0.004 0.051 1495 Dihedral : 13.899 118.386 3599 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.65 % Allowed : 2.59 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1050 helix: 0.14 (0.23), residues: 474 sheet: 0.21 (0.38), residues: 190 loop : -1.23 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS B 63 PHE 0.012 0.001 PHE A 110 TYR 0.012 0.001 TYR B 80 ARG 0.003 0.000 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 151 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.7343 (tt) cc_final: 0.7106 (tt) REVERT: A 99 TYR cc_start: 0.6238 (m-80) cc_final: 0.5510 (m-80) REVERT: B 265 GLN cc_start: 0.7808 (pt0) cc_final: 0.7555 (pt0) REVERT: B 303 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7776 (tm-30) REVERT: C 19 ARG cc_start: 0.7431 (ttp-110) cc_final: 0.7226 (ttm110) REVERT: C 247 ASP cc_start: 0.7316 (m-30) cc_final: 0.7008 (m-30) REVERT: C 258 ASP cc_start: 0.7898 (t0) cc_final: 0.6964 (t0) outliers start: 6 outliers final: 4 residues processed: 154 average time/residue: 1.3217 time to fit residues: 215.5573 Evaluate side-chains 108 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 115 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 0.0170 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 HIS B 82 ASN B 88 GLN B 162 ASN B 176 GLN B 287 HIS ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8896 Z= 0.175 Angle : 0.545 7.103 12086 Z= 0.284 Chirality : 0.043 0.187 1385 Planarity : 0.004 0.047 1495 Dihedral : 7.872 79.227 1591 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.59 % Allowed : 10.02 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1050 helix: 1.52 (0.24), residues: 470 sheet: 0.35 (0.37), residues: 183 loop : -1.19 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.013 0.001 HIS B 63 PHE 0.012 0.001 PHE A 110 TYR 0.015 0.001 TYR A 312 ARG 0.004 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ASP cc_start: 0.7719 (m-30) cc_final: 0.7499 (t70) REVERT: B 105 HIS cc_start: 0.2175 (OUTLIER) cc_final: 0.1373 (m90) REVERT: B 265 GLN cc_start: 0.7742 (pt0) cc_final: 0.7527 (pt0) REVERT: B 287 HIS cc_start: 0.7332 (m-70) cc_final: 0.7014 (m90) REVERT: B 299 GLN cc_start: 0.7520 (tt0) cc_final: 0.7143 (tm-30) REVERT: B 303 GLN cc_start: 0.7482 (tm-30) cc_final: 0.7075 (tm-30) REVERT: B 333 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7413 (t0) REVERT: C 19 ARG cc_start: 0.7308 (ttp-110) cc_final: 0.7106 (ttm110) REVERT: C 176 GLN cc_start: 0.7813 (pt0) cc_final: 0.7550 (pt0) REVERT: C 247 ASP cc_start: 0.7322 (m-30) cc_final: 0.7006 (m-30) REVERT: C 258 ASP cc_start: 0.7986 (t0) cc_final: 0.6989 (t0) outliers start: 24 outliers final: 15 residues processed: 117 average time/residue: 1.2819 time to fit residues: 159.8979 Evaluate side-chains 109 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain D residue 31 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 92 optimal weight: 0.2980 chunk 31 optimal weight: 0.0870 chunk 75 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8896 Z= 0.157 Angle : 0.482 7.171 12086 Z= 0.252 Chirality : 0.041 0.147 1385 Planarity : 0.003 0.042 1495 Dihedral : 7.176 72.501 1589 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.59 % Allowed : 12.18 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1050 helix: 1.98 (0.24), residues: 472 sheet: 0.45 (0.38), residues: 182 loop : -1.25 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.002 0.000 HIS B 327 PHE 0.012 0.001 PHE A 110 TYR 0.012 0.001 TYR A 312 ARG 0.003 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 HIS cc_start: 0.2186 (OUTLIER) cc_final: 0.1418 (m90) REVERT: B 265 GLN cc_start: 0.7764 (pt0) cc_final: 0.7537 (pt0) REVERT: B 287 HIS cc_start: 0.7492 (m-70) cc_final: 0.7169 (m90) REVERT: B 299 GLN cc_start: 0.7472 (tt0) cc_final: 0.7099 (tm-30) REVERT: B 303 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7205 (tm-30) REVERT: C 247 ASP cc_start: 0.7451 (m-30) cc_final: 0.7062 (m-30) REVERT: C 258 ASP cc_start: 0.7954 (t0) cc_final: 0.6960 (t0) outliers start: 24 outliers final: 14 residues processed: 120 average time/residue: 1.2765 time to fit residues: 163.1934 Evaluate side-chains 114 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain B residue 90 MET Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 268 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 48 optimal weight: 0.0010 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 58 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8896 Z= 0.178 Angle : 0.481 7.328 12086 Z= 0.249 Chirality : 0.041 0.134 1385 Planarity : 0.003 0.041 1495 Dihedral : 6.599 53.383 1586 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.66 % Allowed : 13.90 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1050 helix: 2.05 (0.24), residues: 473 sheet: 0.47 (0.38), residues: 181 loop : -1.32 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS B 327 PHE 0.013 0.001 PHE A 110 TYR 0.015 0.001 TYR A 56 ARG 0.003 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 102 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 HIS cc_start: 0.2100 (OUTLIER) cc_final: 0.1433 (m90) REVERT: B 265 GLN cc_start: 0.7822 (pt0) cc_final: 0.7596 (pt0) REVERT: B 287 HIS cc_start: 0.7492 (m-70) cc_final: 0.7172 (m90) REVERT: B 299 GLN cc_start: 0.7515 (tt0) cc_final: 0.7125 (tm-30) REVERT: B 303 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7209 (tm-30) REVERT: C 247 ASP cc_start: 0.7458 (m-30) cc_final: 0.7100 (m-30) REVERT: C 258 ASP cc_start: 0.7966 (t0) cc_final: 0.6925 (t0) outliers start: 34 outliers final: 19 residues processed: 119 average time/residue: 1.2201 time to fit residues: 154.7464 Evaluate side-chains 113 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 315 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 84 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8896 Z= 0.201 Angle : 0.491 7.043 12086 Z= 0.256 Chirality : 0.042 0.146 1385 Planarity : 0.003 0.041 1495 Dihedral : 6.314 53.795 1583 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.56 % Allowed : 14.66 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1050 helix: 1.97 (0.24), residues: 480 sheet: 0.50 (0.37), residues: 181 loop : -1.31 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS C 225 PHE 0.013 0.001 PHE A 110 TYR 0.009 0.001 TYR A 26 ARG 0.003 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 98 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 HIS cc_start: 0.2019 (OUTLIER) cc_final: 0.1388 (m90) REVERT: B 265 GLN cc_start: 0.7825 (pt0) cc_final: 0.7599 (pt0) REVERT: B 287 HIS cc_start: 0.7535 (m-70) cc_final: 0.7214 (m90) REVERT: B 299 GLN cc_start: 0.7539 (tt0) cc_final: 0.7128 (tm-30) REVERT: B 303 GLN cc_start: 0.7614 (tm-30) cc_final: 0.7270 (tm-30) REVERT: C 247 ASP cc_start: 0.7445 (m-30) cc_final: 0.7089 (m-30) REVERT: C 258 ASP cc_start: 0.8002 (t0) cc_final: 0.6921 (t0) outliers start: 33 outliers final: 25 residues processed: 115 average time/residue: 1.2858 time to fit residues: 157.1737 Evaluate side-chains 121 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 315 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8896 Z= 0.260 Angle : 0.524 7.139 12086 Z= 0.273 Chirality : 0.043 0.136 1385 Planarity : 0.004 0.041 1495 Dihedral : 6.371 54.300 1583 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.99 % Allowed : 14.66 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.26), residues: 1050 helix: 1.84 (0.24), residues: 479 sheet: 0.38 (0.37), residues: 183 loop : -1.31 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS B 327 PHE 0.014 0.002 PHE A 110 TYR 0.014 0.001 TYR A 56 ARG 0.003 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 97 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 HIS cc_start: 0.2040 (OUTLIER) cc_final: 0.1447 (m90) REVERT: B 265 GLN cc_start: 0.7830 (pt0) cc_final: 0.7607 (pt0) REVERT: B 287 HIS cc_start: 0.7488 (m-70) cc_final: 0.7163 (m90) REVERT: B 299 GLN cc_start: 0.7575 (tt0) cc_final: 0.7114 (tm-30) REVERT: B 303 GLN cc_start: 0.7503 (tm-30) cc_final: 0.7107 (tm-30) REVERT: C 46 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6692 (mtp-110) REVERT: C 247 ASP cc_start: 0.7338 (m-30) cc_final: 0.7104 (m-30) REVERT: C 258 ASP cc_start: 0.8079 (t0) cc_final: 0.7021 (t0) outliers start: 37 outliers final: 26 residues processed: 115 average time/residue: 1.2048 time to fit residues: 147.9434 Evaluate side-chains 121 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 315 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 83 optimal weight: 0.0570 chunk 55 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 45 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 GLN D 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8896 Z= 0.142 Angle : 0.461 7.000 12086 Z= 0.240 Chirality : 0.040 0.144 1385 Planarity : 0.003 0.040 1495 Dihedral : 5.974 53.373 1583 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.91 % Allowed : 16.38 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1050 helix: 2.07 (0.24), residues: 483 sheet: 0.46 (0.37), residues: 184 loop : -1.24 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.002 0.001 HIS A 183 PHE 0.012 0.001 PHE C 199 TYR 0.008 0.001 TYR B 80 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 HIS cc_start: 0.1971 (OUTLIER) cc_final: 0.1440 (m90) REVERT: B 265 GLN cc_start: 0.7813 (pt0) cc_final: 0.7601 (pt0) REVERT: B 303 GLN cc_start: 0.7514 (tm-30) cc_final: 0.7204 (tm-30) REVERT: C 138 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7448 (mm-30) REVERT: C 247 ASP cc_start: 0.7442 (m-30) cc_final: 0.7085 (m-30) REVERT: C 258 ASP cc_start: 0.8012 (t0) cc_final: 0.6921 (t0) outliers start: 27 outliers final: 17 residues processed: 118 average time/residue: 1.1940 time to fit residues: 150.7738 Evaluate side-chains 114 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 315 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 95 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8896 Z= 0.288 Angle : 0.541 8.616 12086 Z= 0.279 Chirality : 0.043 0.142 1385 Planarity : 0.004 0.041 1495 Dihedral : 6.122 54.994 1579 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.34 % Allowed : 16.49 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.26), residues: 1050 helix: 1.84 (0.24), residues: 479 sheet: 0.42 (0.37), residues: 181 loop : -1.32 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.005 0.001 HIS B 327 PHE 0.014 0.002 PHE A 110 TYR 0.013 0.001 TYR A 56 ARG 0.003 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 94 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 HIS cc_start: 0.2137 (OUTLIER) cc_final: 0.1664 (m90) REVERT: B 303 GLN cc_start: 0.7470 (tm-30) cc_final: 0.7073 (tm-30) REVERT: C 46 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6742 (mtp-110) REVERT: C 134 ARG cc_start: 0.6646 (mpt-90) cc_final: 0.6372 (mpt-90) REVERT: C 247 ASP cc_start: 0.7365 (m-30) cc_final: 0.7144 (m-30) REVERT: C 258 ASP cc_start: 0.8085 (t0) cc_final: 0.6977 (t0) outliers start: 31 outliers final: 21 residues processed: 111 average time/residue: 1.2343 time to fit residues: 146.2221 Evaluate side-chains 114 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 315 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 95 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 40.0000 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 GLN B 287 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8896 Z= 0.183 Angle : 0.508 8.082 12086 Z= 0.261 Chirality : 0.041 0.146 1385 Planarity : 0.003 0.041 1495 Dihedral : 5.957 55.609 1579 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.34 % Allowed : 16.92 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1050 helix: 1.96 (0.24), residues: 483 sheet: 0.31 (0.37), residues: 186 loop : -1.25 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.002 0.001 HIS L 6 PHE 0.012 0.001 PHE A 110 TYR 0.008 0.001 TYR A 26 ARG 0.004 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 97 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ILE cc_start: 0.7489 (tp) cc_final: 0.7174 (pt) REVERT: A 15 GLN cc_start: 0.7853 (pt0) cc_final: 0.7552 (pt0) REVERT: B 105 HIS cc_start: 0.2109 (OUTLIER) cc_final: 0.1614 (m90) REVERT: B 303 GLN cc_start: 0.7415 (tm-30) cc_final: 0.7037 (tm-30) REVERT: C 134 ARG cc_start: 0.6709 (OUTLIER) cc_final: 0.6464 (mpt-90) REVERT: C 138 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7437 (mm-30) REVERT: C 247 ASP cc_start: 0.7342 (m-30) cc_final: 0.7096 (m-30) REVERT: C 258 ASP cc_start: 0.8064 (t0) cc_final: 0.6965 (t0) outliers start: 31 outliers final: 24 residues processed: 114 average time/residue: 1.2312 time to fit residues: 149.6615 Evaluate side-chains 118 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8896 Z= 0.326 Angle : 0.582 9.158 12086 Z= 0.300 Chirality : 0.044 0.136 1385 Planarity : 0.004 0.041 1495 Dihedral : 6.233 54.451 1579 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.91 % Allowed : 17.56 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 1050 helix: 1.73 (0.24), residues: 479 sheet: 0.17 (0.37), residues: 186 loop : -1.32 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.005 0.001 HIS B 327 PHE 0.014 0.002 PHE C 234 TYR 0.016 0.002 TYR A 56 ARG 0.007 0.000 ARG C 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ILE cc_start: 0.7612 (tp) cc_final: 0.7299 (pt) REVERT: B 105 HIS cc_start: 0.2162 (OUTLIER) cc_final: 0.1675 (m90) REVERT: B 299 GLN cc_start: 0.7499 (tt0) cc_final: 0.7240 (tp40) REVERT: B 303 GLN cc_start: 0.7507 (tm-30) cc_final: 0.7107 (tm-30) REVERT: C 134 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.6484 (mpt180) REVERT: C 258 ASP cc_start: 0.8122 (t0) cc_final: 0.6997 (t0) outliers start: 27 outliers final: 23 residues processed: 107 average time/residue: 1.3281 time to fit residues: 151.1878 Evaluate side-chains 112 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 87 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain B residue 105 HIS Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 17 GLN Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 315 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.172543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.111199 restraints weight = 9358.252| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.48 r_work: 0.3140 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8896 Z= 0.176 Angle : 0.517 7.699 12086 Z= 0.268 Chirality : 0.042 0.262 1385 Planarity : 0.004 0.041 1495 Dihedral : 5.978 55.170 1579 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.91 % Allowed : 17.67 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1050 helix: 1.91 (0.24), residues: 482 sheet: 0.18 (0.37), residues: 187 loop : -1.26 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.002 0.001 HIS L 6 PHE 0.013 0.001 PHE A 96 TYR 0.008 0.001 TYR A 26 ARG 0.007 0.000 ARG C 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3254.93 seconds wall clock time: 58 minutes 37.74 seconds (3517.74 seconds total)