Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 21:30:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6g_31479/08_2023/7f6g_31479_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6g_31479/08_2023/7f6g_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_31479/08_2023/7f6g_31479.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6g_31479/08_2023/7f6g_31479.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6g_31479/08_2023/7f6g_31479_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f6g_31479/08_2023/7f6g_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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 chiralities: 1 Time building chain proxies: 4.67, per 1000 atoms: 0.54 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: 3.27 Conformation dependent library (CDL) restraints added in 1.4 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: 1.24 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: 2.35 Time building geometry restraints manager: 3.49 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: 4988 23.68 - 47.35: 250 47.35 - 71.03: 27 71.03 - 94.71: 3 94.71 - 118.39: 2 Dihedral angle restraints: 5270 sinusoidal: 2148 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 5267 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: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 3.640 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.930 Find NCS groups from input model: 0.260 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:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.110 ------------------------------------------------------------------------------- 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 : 13.575 118.386 3242 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 % 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 *********************** 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 : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 154 average time/residue: 1.3222 time to fit residues: 215.6414 Evaluate side-chains 107 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 2 average time/residue: 0.7051 time to fit residues: 2.8167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 0.0170 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 265 GLN B 287 HIS ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8896 Z= 0.184 Angle : 0.544 7.088 12086 Z= 0.287 Chirality : 0.042 0.195 1385 Planarity : 0.004 0.047 1495 Dihedral : 6.161 112.832 1222 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 2.69 % 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: 0.47 (0.25), residues: 1050 helix: 1.53 (0.24), residues: 470 sheet: 0.31 (0.38), residues: 185 loop : -1.17 (0.28), residues: 395 *********************** 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 127 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 116 average time/residue: 1.3288 time to fit residues: 163.9310 Evaluate side-chains 108 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 8 residues processed: 7 average time/residue: 0.4715 time to fit residues: 5.2031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.0570 chunk 29 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 83 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 31 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 265 GLN B 299 GLN C 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 8896 Z= 0.139 Angle : 0.477 7.535 12086 Z= 0.249 Chirality : 0.040 0.139 1385 Planarity : 0.004 0.042 1495 Dihedral : 5.709 115.009 1222 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 2.26 % 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: 0.88 (0.26), residues: 1050 helix: 2.08 (0.24), residues: 470 sheet: 0.47 (0.38), residues: 182 loop : -1.23 (0.28), residues: 398 *********************** 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: 21 poor density : 110 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 121 average time/residue: 1.2744 time to fit residues: 164.1914 Evaluate side-chains 110 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 3 average time/residue: 0.0899 time to fit residues: 1.7158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 265 GLN B 299 GLN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8896 Z= 0.192 Angle : 0.495 7.097 12086 Z= 0.257 Chirality : 0.041 0.137 1385 Planarity : 0.004 0.042 1495 Dihedral : 5.603 113.663 1222 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 3.88 % 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: 0.86 (0.26), residues: 1050 helix: 2.08 (0.24), residues: 473 sheet: 0.46 (0.38), residues: 181 loop : -1.31 (0.28), residues: 396 *********************** 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 137 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 101 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 20 residues processed: 118 average time/residue: 1.2407 time to fit residues: 156.0791 Evaluate side-chains 114 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.953 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 9 residues processed: 11 average time/residue: 0.3236 time to fit residues: 5.6719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 74 optimal weight: 0.0970 chunk 41 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 GLN B 299 GLN C 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8896 Z= 0.166 Angle : 0.479 8.628 12086 Z= 0.248 Chirality : 0.041 0.147 1385 Planarity : 0.003 0.041 1495 Dihedral : 5.511 113.684 1222 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1050 helix: 2.07 (0.24), residues: 479 sheet: 0.45 (0.37), residues: 182 loop : -1.26 (0.29), residues: 389 *********************** 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 122 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 111 average time/residue: 1.3480 time to fit residues: 159.1820 Evaluate side-chains 109 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 5 average time/residue: 0.3589 time to fit residues: 3.4270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 GLN ** 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: 0.7584 moved from start: 0.2188 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= 0.231 Angle : 0.514 8.193 12086 Z= 0.265 Chirality : 0.042 0.138 1385 Planarity : 0.004 0.042 1495 Dihedral : 5.590 113.270 1222 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 3.45 % 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: 1.97 (0.24), residues: 479 sheet: 0.47 (0.37), residues: 181 loop : -1.25 (0.29), residues: 390 *********************** 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 127 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 95 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 24 residues processed: 111 average time/residue: 1.3232 time to fit residues: 156.8485 Evaluate side-chains 118 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 13 residues processed: 11 average time/residue: 0.1684 time to fit residues: 4.8659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2279 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= 0.230 Angle : 0.516 9.432 12086 Z= 0.267 Chirality : 0.042 0.139 1385 Planarity : 0.004 0.042 1495 Dihedral : 5.636 113.021 1222 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 3.12 % 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: 1.94 (0.24), residues: 479 sheet: 0.42 (0.37), residues: 181 loop : -1.24 (0.29), residues: 390 *********************** 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 125 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 96 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 19 residues processed: 115 average time/residue: 1.3041 time to fit residues: 159.8414 Evaluate side-chains 112 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 13 residues processed: 6 average time/residue: 0.5212 time to fit residues: 4.8361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 8.9990 chunk 59 optimal weight: 0.0270 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 HIS ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2353 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= 0.199 Angle : 0.508 8.692 12086 Z= 0.263 Chirality : 0.042 0.143 1385 Planarity : 0.004 0.042 1495 Dihedral : 5.594 113.033 1222 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 2.37 % 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: 0.91 (0.26), residues: 1050 helix: 2.03 (0.24), residues: 483 sheet: 0.43 (0.37), residues: 181 loop : -1.21 (0.29), residues: 386 *********************** 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 116 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 18 residues processed: 109 average time/residue: 1.2945 time to fit residues: 150.3236 Evaluate side-chains 109 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.949 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 5 average time/residue: 0.1029 time to fit residues: 2.1924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 95 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 30.0000 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2365 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= 0.263 Angle : 0.549 8.865 12086 Z= 0.284 Chirality : 0.043 0.141 1385 Planarity : 0.004 0.042 1495 Dihedral : 5.710 112.623 1222 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 2.16 % 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: 1.87 (0.24), residues: 479 sheet: 0.42 (0.37), residues: 178 loop : -1.27 (0.29), residues: 393 *********************** 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 114 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 17 residues processed: 108 average time/residue: 1.3467 time to fit residues: 154.5523 Evaluate side-chains 109 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.884 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.1491 time to fit residues: 2.0786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.0870 chunk 46 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8896 Z= 0.172 Angle : 0.513 8.379 12086 Z= 0.266 Chirality : 0.041 0.130 1385 Planarity : 0.004 0.041 1495 Dihedral : 5.591 112.872 1222 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 1.94 % 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: 0.87 (0.26), residues: 1050 helix: 2.00 (0.24), residues: 484 sheet: 0.41 (0.37), residues: 181 loop : -1.22 (0.29), residues: 385 ********************** 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 115 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 112 average time/residue: 1.3469 time to fit residues: 160.6206 Evaluate side-chains 109 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.0781 time to fit residues: 1.5742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.172192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117250 restraints weight = 9396.380| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.80 r_work: 0.3091 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2479 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= 0.219 Angle : 0.535 8.534 12086 Z= 0.277 Chirality : 0.042 0.132 1385 Planarity : 0.004 0.042 1495 Dihedral : 5.630 112.590 1222 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 1.94 % 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: 0.78 (0.26), residues: 1050 helix: 1.95 (0.24), residues: 480 sheet: 0.36 (0.37), residues: 181 loop : -1.27 (0.29), residues: 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3182.96 seconds wall clock time: 57 minutes 20.35 seconds (3440.35 seconds total)