Starting phenix.real_space_refine on Fri Jul 19 08:39:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpp_36486/07_2024/8jpp_36486.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpp_36486/07_2024/8jpp_36486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpp_36486/07_2024/8jpp_36486.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpp_36486/07_2024/8jpp_36486.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpp_36486/07_2024/8jpp_36486.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jpp_36486/07_2024/8jpp_36486.cif" } resolution = 3.2 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= -0.002 sd= 0.047 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 41 5.16 5 C 4565 2.51 5 N 1228 2.21 5 O 1303 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "R GLU 22": "OE1" <-> "OE2" Residue "R GLU 33": "OE1" <-> "OE2" Residue "R ASP 119": "OD1" <-> "OD2" Residue "R GLU 153": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7137 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1897 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 2511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2511 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 325} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 376 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 44} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2345 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 12, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 81 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SIN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.90, per 1000 atoms: 0.69 Number of scatterers: 7137 At special positions: 0 Unit cell: (74.048, 99.84, 132.288, 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 41 16.00 O 1303 8.00 N 1228 7.00 C 4565 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 268 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 172 " 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 Time building additional restraints: 3.02 Conformation dependent library (CDL) restraints added in 1.2 seconds 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1748 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 47.0% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.591A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 241 removed outlier: 4.477A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 268 Processing helix chain 'A' and resid 283 through 293 Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.024A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 Processing helix chain 'A' and resid 321 through 341 Processing helix chain 'A' and resid 360 through 381 Processing helix chain 'B' and resid 11 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 15 through 24 removed outlier: 3.742A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 11 through 50 removed outlier: 4.260A pdb=" N LEU R 26 " --> pdb=" O GLU R 22 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER R 27 " --> pdb=" O LYS R 23 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU R 39 " --> pdb=" O VAL R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 75 removed outlier: 3.507A pdb=" N THR R 75 " --> pdb=" O ALA R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 86 removed outlier: 4.541A pdb=" N LEU R 79 " --> pdb=" O THR R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 126 removed outlier: 4.173A pdb=" N LEU R 94 " --> pdb=" O TYR R 90 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS R 95 " --> pdb=" O GLY R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 154 Processing helix chain 'R' and resid 157 through 162 Processing helix chain 'R' and resid 180 through 196 removed outlier: 3.510A pdb=" N TYR R 187 " --> pdb=" O TYR R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 221 Processing helix chain 'R' and resid 227 through 258 removed outlier: 3.560A pdb=" N LEU R 231 " --> pdb=" O LEU R 227 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) Proline residue: R 247 - end of helix removed outlier: 3.582A pdb=" N VAL R 254 " --> pdb=" O VAL R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 285 removed outlier: 3.558A pdb=" N THR R 280 " --> pdb=" O PHE R 276 " (cutoff:3.500A) Proline residue: R 282 - end of helix Processing helix chain 'R' and resid 286 through 296 Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 301 through 317 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.525A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 50 removed outlier: 6.841A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.612A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.278A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.317A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.584A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.572A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.720A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1131 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: 2.12 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1162 1.32 - 1.44: 2021 1.44 - 1.56: 4049 1.56 - 1.69: 0 1.69 - 1.81: 57 Bond restraints: 7289 Sorted by residual: bond pdb=" C LEU R 185 " pdb=" O LEU R 185 " ideal model delta sigma weight residual 1.234 1.195 0.040 1.17e-02 7.31e+03 1.17e+01 bond pdb=" C PRO R 181 " pdb=" O PRO R 181 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.29e-02 6.01e+03 8.54e+00 bond pdb=" N ILE R 118 " pdb=" CA ILE R 118 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.41e-02 5.03e+03 8.10e+00 bond pdb=" CA SER A 250 " pdb=" CB SER A 250 " ideal model delta sigma weight residual 1.530 1.482 0.048 1.75e-02 3.27e+03 7.61e+00 bond pdb=" N ILE R 89 " pdb=" CA ILE R 89 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.03e+00 ... (remaining 7284 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.30: 149 106.30 - 113.28: 3954 113.28 - 120.27: 2752 120.27 - 127.25: 2983 127.25 - 134.24: 75 Bond angle restraints: 9913 Sorted by residual: angle pdb=" N LEU A 262 " pdb=" CA LEU A 262 " pdb=" C LEU A 262 " ideal model delta sigma weight residual 112.23 104.47 7.76 1.26e+00 6.30e-01 3.80e+01 angle pdb=" N ASN R 184 " pdb=" CA ASN R 184 " pdb=" C ASN R 184 " ideal model delta sigma weight residual 113.18 106.47 6.71 1.21e+00 6.83e-01 3.08e+01 angle pdb=" N ARG R 120 " pdb=" CA ARG R 120 " pdb=" C ARG R 120 " ideal model delta sigma weight residual 112.23 106.54 5.69 1.26e+00 6.30e-01 2.04e+01 angle pdb=" CA PHE A 208 " pdb=" CB PHE A 208 " pdb=" CG PHE A 208 " ideal model delta sigma weight residual 113.80 117.96 -4.16 1.00e+00 1.00e+00 1.73e+01 angle pdb=" N LEU A 260 " pdb=" CA LEU A 260 " pdb=" C LEU A 260 " ideal model delta sigma weight residual 112.54 107.55 4.99 1.22e+00 6.72e-01 1.68e+01 ... (remaining 9908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 3801 17.36 - 34.71: 388 34.71 - 52.06: 99 52.06 - 69.42: 10 69.42 - 86.77: 8 Dihedral angle restraints: 4306 sinusoidal: 1606 harmonic: 2700 Sorted by residual: dihedral pdb=" CD ARG A 61 " pdb=" NE ARG A 61 " pdb=" CZ ARG A 61 " pdb=" NH1 ARG A 61 " ideal model delta sinusoidal sigma weight residual 0.00 -28.40 28.40 1 1.00e+01 1.00e-02 1.16e+01 dihedral pdb=" CA ASP R 119 " pdb=" CB ASP R 119 " pdb=" CG ASP R 119 " pdb=" OD1 ASP R 119 " ideal model delta sinusoidal sigma weight residual -30.00 -85.50 55.50 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CG ARG R 303 " pdb=" CD ARG R 303 " pdb=" NE ARG R 303 " pdb=" CZ ARG R 303 " ideal model delta sinusoidal sigma weight residual -90.00 -133.94 43.94 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 4303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 822 0.038 - 0.076: 206 0.076 - 0.114: 81 0.114 - 0.152: 27 0.152 - 0.190: 3 Chirality restraints: 1139 Sorted by residual: chirality pdb=" CA ILE R 186 " pdb=" N ILE R 186 " pdb=" C ILE R 186 " pdb=" CB ILE R 186 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CB VAL R 38 " pdb=" CA VAL R 38 " pdb=" CG1 VAL R 38 " pdb=" CG2 VAL R 38 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CA ILE R 89 " pdb=" N ILE R 89 " pdb=" C ILE R 89 " pdb=" CB ILE R 89 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.66e-01 ... (remaining 1136 not shown) Planarity restraints: 1265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 61 " -0.519 9.50e-02 1.11e+02 2.33e-01 3.30e+01 pdb=" NE ARG A 61 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 61 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 61 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 61 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 120 " 0.260 9.50e-02 1.11e+02 1.17e-01 8.34e+00 pdb=" NE ARG R 120 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG R 120 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG R 120 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG R 120 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 232 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C ILE B 232 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE B 232 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS B 233 " -0.010 2.00e-02 2.50e+03 ... (remaining 1262 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1255 2.76 - 3.29: 7449 3.29 - 3.83: 12170 3.83 - 4.36: 14863 4.36 - 4.90: 25806 Nonbonded interactions: 61543 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.223 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.232 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.233 2.440 nonbonded pdb=" N GLU G 47 " pdb=" OE1 GLU G 47 " model vdw 2.236 2.520 nonbonded pdb=" O LEU R 39 " pdb=" OG1 THR R 42 " model vdw 2.257 2.440 ... (remaining 61538 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: 2.550 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.660 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.004 0.048 7289 Z= 0.257 Angle : 0.652 7.764 9913 Z= 0.418 Chirality : 0.043 0.190 1139 Planarity : 0.008 0.233 1265 Dihedral : 15.093 86.773 2552 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.68 % Allowed : 16.01 % Favored : 83.31 % 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: -0.08 (0.29), residues: 910 helix: 1.32 (0.28), residues: 407 sheet: -1.88 (0.35), residues: 173 loop : -0.60 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 263 HIS 0.004 0.001 HIS A 220 PHE 0.025 0.002 PHE A 208 TYR 0.012 0.001 TYR R 107 ARG 0.009 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 145 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7411 (mpt180) cc_final: 0.6551 (mtm-85) REVERT: A 21 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7157 (tm-30) REVERT: A 220 HIS cc_start: 0.7716 (t-170) cc_final: 0.6985 (t-170) REVERT: A 376 MET cc_start: 0.7941 (ttm) cc_final: 0.7645 (ttt) REVERT: B 292 PHE cc_start: 0.8634 (m-10) cc_final: 0.8272 (m-80) REVERT: B 329 THR cc_start: 0.9005 (m) cc_final: 0.8545 (p) outliers start: 5 outliers final: 2 residues processed: 149 average time/residue: 0.2267 time to fit residues: 43.5558 Evaluate side-chains 123 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.9990 chunk 68 optimal weight: 0.0770 chunk 37 optimal weight: 0.3980 chunk 23 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN R 184 ASN R 270 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7289 Z= 0.220 Angle : 0.540 6.750 9913 Z= 0.284 Chirality : 0.043 0.221 1139 Planarity : 0.004 0.036 1265 Dihedral : 5.102 48.728 1012 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.66 % Allowed : 14.65 % Favored : 81.68 % 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: 0.41 (0.28), residues: 910 helix: 1.80 (0.26), residues: 406 sheet: -1.58 (0.36), residues: 166 loop : -0.53 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 263 HIS 0.003 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.021 0.001 TYR R 187 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7341 (mpt180) cc_final: 0.6522 (mtm-85) REVERT: A 24 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8150 (pttm) REVERT: B 292 PHE cc_start: 0.8737 (m-10) cc_final: 0.8435 (m-80) REVERT: R 33 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7955 (mt-10) outliers start: 27 outliers final: 15 residues processed: 147 average time/residue: 0.2008 time to fit residues: 39.4374 Evaluate side-chains 134 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 243 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN R 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7289 Z= 0.273 Angle : 0.541 5.683 9913 Z= 0.283 Chirality : 0.044 0.215 1139 Planarity : 0.004 0.035 1265 Dihedral : 4.644 50.614 1008 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.75 % Allowed : 15.47 % Favored : 79.78 % 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: 0.49 (0.28), residues: 910 helix: 1.94 (0.26), residues: 406 sheet: -1.68 (0.35), residues: 173 loop : -0.47 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 263 HIS 0.003 0.001 HIS R 131 PHE 0.014 0.002 PHE A 222 TYR 0.018 0.001 TYR R 187 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 133 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8831 (OUTLIER) cc_final: 0.8558 (p0) REVERT: B 258 ASP cc_start: 0.7630 (t0) cc_final: 0.7346 (t0) REVERT: B 292 PHE cc_start: 0.8775 (m-10) cc_final: 0.8534 (m-80) REVERT: R 33 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8099 (mt-10) outliers start: 35 outliers final: 22 residues processed: 154 average time/residue: 0.1865 time to fit residues: 38.6510 Evaluate side-chains 141 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 204 CYS Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 250 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7289 Z= 0.254 Angle : 0.536 7.795 9913 Z= 0.279 Chirality : 0.044 0.206 1139 Planarity : 0.004 0.040 1265 Dihedral : 4.637 51.417 1008 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.75 % Allowed : 16.82 % Favored : 78.43 % 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 (0.28), residues: 910 helix: 2.04 (0.26), residues: 406 sheet: -1.73 (0.35), residues: 175 loop : -0.47 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 263 HIS 0.004 0.001 HIS R 131 PHE 0.013 0.002 PHE R 115 TYR 0.016 0.001 TYR R 187 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 122 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8516 (p0) REVERT: B 258 ASP cc_start: 0.7702 (t0) cc_final: 0.7368 (t0) REVERT: B 262 MET cc_start: 0.7781 (ttm) cc_final: 0.7354 (mmt) REVERT: G 58 GLU cc_start: 0.6608 (pm20) cc_final: 0.6378 (pm20) REVERT: R 33 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8169 (mt-10) outliers start: 35 outliers final: 25 residues processed: 145 average time/residue: 0.1884 time to fit residues: 36.6567 Evaluate side-chains 142 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 250 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 0.2980 chunk 60 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7289 Z= 0.176 Angle : 0.510 6.253 9913 Z= 0.264 Chirality : 0.043 0.218 1139 Planarity : 0.004 0.039 1265 Dihedral : 4.487 51.494 1008 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.75 % Allowed : 17.23 % Favored : 78.02 % 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: 0.72 (0.29), residues: 910 helix: 2.14 (0.26), residues: 412 sheet: -1.67 (0.34), residues: 175 loop : -0.36 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 263 HIS 0.003 0.001 HIS R 131 PHE 0.016 0.001 PHE B 292 TYR 0.020 0.001 TYR R 187 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7086 (mpt180) cc_final: 0.5775 (mtm-85) REVERT: A 218 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8520 (p0) REVERT: B 198 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8402 (pp) REVERT: B 258 ASP cc_start: 0.7646 (t0) cc_final: 0.7298 (t0) REVERT: B 262 MET cc_start: 0.7682 (ttm) cc_final: 0.7289 (mmt) REVERT: B 292 PHE cc_start: 0.8562 (m-80) cc_final: 0.8188 (m-80) REVERT: R 33 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8156 (mt-10) outliers start: 35 outliers final: 22 residues processed: 146 average time/residue: 0.1964 time to fit residues: 38.5821 Evaluate side-chains 140 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 125 LYS Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 204 CYS Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 246 THR Chi-restraints excluded: chain R residue 250 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7289 Z= 0.240 Angle : 0.537 6.281 9913 Z= 0.276 Chirality : 0.044 0.235 1139 Planarity : 0.004 0.038 1265 Dihedral : 4.609 53.531 1008 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.88 % Allowed : 17.91 % Favored : 77.20 % 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: 0.67 (0.28), residues: 910 helix: 2.08 (0.26), residues: 412 sheet: -1.68 (0.34), residues: 174 loop : -0.36 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 263 HIS 0.004 0.001 HIS R 131 PHE 0.016 0.002 PHE A 222 TYR 0.017 0.001 TYR R 187 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 122 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7057 (mpt180) cc_final: 0.5769 (mtm-85) REVERT: A 38 ARG cc_start: 0.8356 (mmm-85) cc_final: 0.8092 (mtp85) REVERT: A 218 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8492 (p0) REVERT: A 300 ASP cc_start: 0.6939 (OUTLIER) cc_final: 0.6363 (t0) REVERT: B 198 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8397 (pp) REVERT: B 258 ASP cc_start: 0.7677 (t0) cc_final: 0.7267 (t0) REVERT: B 292 PHE cc_start: 0.8586 (m-80) cc_final: 0.8224 (m-80) REVERT: B 325 MET cc_start: 0.8378 (tpp) cc_final: 0.8139 (mmt) REVERT: B 329 THR cc_start: 0.8888 (m) cc_final: 0.8429 (p) REVERT: R 33 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8226 (mt-10) outliers start: 36 outliers final: 26 residues processed: 146 average time/residue: 0.1879 time to fit residues: 36.9239 Evaluate side-chains 147 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 118 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 204 CYS Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 250 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7289 Z= 0.243 Angle : 0.544 6.820 9913 Z= 0.280 Chirality : 0.044 0.240 1139 Planarity : 0.004 0.038 1265 Dihedral : 4.632 54.003 1008 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.88 % Allowed : 19.54 % Favored : 75.58 % 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: 0.62 (0.28), residues: 910 helix: 2.08 (0.26), residues: 411 sheet: -1.72 (0.34), residues: 174 loop : -0.43 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 263 HIS 0.003 0.001 HIS R 131 PHE 0.015 0.002 PHE R 294 TYR 0.017 0.001 TYR R 187 ARG 0.007 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 120 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7032 (mpt180) cc_final: 0.5823 (mtm-85) REVERT: A 218 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8489 (p0) REVERT: A 300 ASP cc_start: 0.6973 (OUTLIER) cc_final: 0.6365 (t0) REVERT: B 198 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8431 (pp) REVERT: B 258 ASP cc_start: 0.7709 (t0) cc_final: 0.7209 (t0) REVERT: B 292 PHE cc_start: 0.8625 (m-80) cc_final: 0.8261 (m-80) REVERT: B 329 THR cc_start: 0.8905 (m) cc_final: 0.8437 (p) REVERT: G 21 MET cc_start: 0.7565 (ptm) cc_final: 0.7294 (ppp) REVERT: G 58 GLU cc_start: 0.6535 (pm20) cc_final: 0.6279 (pm20) REVERT: R 33 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8230 (mt-10) outliers start: 36 outliers final: 26 residues processed: 145 average time/residue: 0.1821 time to fit residues: 35.6527 Evaluate side-chains 143 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 204 CYS Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 250 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 chunk 78 optimal weight: 0.0000 chunk 83 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7289 Z= 0.179 Angle : 0.533 8.965 9913 Z= 0.273 Chirality : 0.043 0.217 1139 Planarity : 0.004 0.037 1265 Dihedral : 4.557 55.018 1008 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.93 % Allowed : 20.49 % Favored : 75.58 % 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: 0.66 (0.28), residues: 910 helix: 2.08 (0.26), residues: 412 sheet: -1.63 (0.34), residues: 174 loop : -0.42 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 263 HIS 0.003 0.001 HIS B 54 PHE 0.015 0.001 PHE R 294 TYR 0.015 0.001 TYR R 187 ARG 0.006 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 124 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.6974 (mpt180) cc_final: 0.5849 (mtm-85) REVERT: A 218 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8455 (p0) REVERT: A 300 ASP cc_start: 0.6878 (OUTLIER) cc_final: 0.6384 (t0) REVERT: A 346 ARG cc_start: 0.7401 (mtm-85) cc_final: 0.7099 (mtm-85) REVERT: B 198 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8442 (pp) REVERT: B 258 ASP cc_start: 0.7704 (t0) cc_final: 0.7197 (t0) REVERT: B 292 PHE cc_start: 0.8584 (m-80) cc_final: 0.8198 (m-80) REVERT: B 329 THR cc_start: 0.8894 (m) cc_final: 0.8447 (p) REVERT: G 21 MET cc_start: 0.7585 (ptm) cc_final: 0.7323 (ppp) REVERT: G 58 GLU cc_start: 0.6479 (pm20) cc_final: 0.6275 (pm20) REVERT: R 33 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8213 (mt-10) outliers start: 29 outliers final: 23 residues processed: 145 average time/residue: 0.1859 time to fit residues: 36.4598 Evaluate side-chains 143 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 204 CYS Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 250 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 0.0370 chunk 35 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.0470 chunk 53 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.5956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 : 0.003 0.059 7289 Z= 0.208 Angle : 0.560 10.443 9913 Z= 0.282 Chirality : 0.043 0.221 1139 Planarity : 0.004 0.037 1265 Dihedral : 4.528 55.035 1008 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.07 % Allowed : 20.22 % Favored : 75.71 % 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: 0.68 (0.29), residues: 910 helix: 2.10 (0.26), residues: 411 sheet: -1.60 (0.35), residues: 174 loop : -0.41 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 263 HIS 0.003 0.001 HIS B 54 PHE 0.016 0.001 PHE R 294 TYR 0.015 0.001 TYR R 187 ARG 0.005 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 218 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8469 (p0) REVERT: A 300 ASP cc_start: 0.6906 (OUTLIER) cc_final: 0.6387 (t0) REVERT: A 346 ARG cc_start: 0.7400 (mtm-85) cc_final: 0.7101 (mtm-85) REVERT: B 198 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8417 (pp) REVERT: B 258 ASP cc_start: 0.7755 (t0) cc_final: 0.7213 (t0) REVERT: B 292 PHE cc_start: 0.8581 (m-80) cc_final: 0.8198 (m-80) REVERT: B 329 THR cc_start: 0.8924 (m) cc_final: 0.8452 (p) REVERT: G 21 MET cc_start: 0.7607 (ptm) cc_final: 0.7349 (ppp) REVERT: R 33 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8239 (mt-10) outliers start: 30 outliers final: 25 residues processed: 141 average time/residue: 0.1811 time to fit residues: 34.6023 Evaluate side-chains 144 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 204 CYS Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 250 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.0040 chunk 89 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 71 optimal weight: 0.0050 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 overall best weight: 0.5208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7289 Z= 0.193 Angle : 0.530 8.229 9913 Z= 0.272 Chirality : 0.043 0.214 1139 Planarity : 0.004 0.037 1265 Dihedral : 4.481 55.278 1008 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.80 % Allowed : 20.22 % Favored : 75.98 % 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: 0.71 (0.29), residues: 910 helix: 2.15 (0.26), residues: 411 sheet: -1.61 (0.35), residues: 174 loop : -0.42 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 263 HIS 0.002 0.001 HIS A 347 PHE 0.016 0.001 PHE R 294 TYR 0.014 0.001 TYR R 187 ARG 0.005 0.000 ARG A 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 123 time to evaluate : 0.778 Fit side-chains REVERT: A 13 ARG cc_start: 0.7191 (mpt180) cc_final: 0.5856 (mtm-85) REVERT: A 218 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8488 (p0) REVERT: A 220 HIS cc_start: 0.7685 (t-170) cc_final: 0.6878 (t-170) REVERT: A 300 ASP cc_start: 0.6855 (OUTLIER) cc_final: 0.6369 (t0) REVERT: A 346 ARG cc_start: 0.7401 (mtm-85) cc_final: 0.7132 (mtm-85) REVERT: B 198 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8426 (pp) REVERT: B 258 ASP cc_start: 0.7767 (t0) cc_final: 0.7221 (t0) REVERT: B 292 PHE cc_start: 0.8547 (m-80) cc_final: 0.8174 (m-80) REVERT: B 329 THR cc_start: 0.8915 (m) cc_final: 0.8455 (p) REVERT: G 21 MET cc_start: 0.7632 (ptm) cc_final: 0.7361 (ppp) REVERT: R 33 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8249 (mt-10) outliers start: 28 outliers final: 23 residues processed: 143 average time/residue: 0.1792 time to fit residues: 35.0901 Evaluate side-chains 144 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 118 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 42 THR Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 204 CYS Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 250 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 0.0870 chunk 13 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.165032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.129040 restraints weight = 9279.438| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.68 r_work: 0.3499 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7289 Z= 0.200 Angle : 0.542 8.320 9913 Z= 0.278 Chirality : 0.043 0.209 1139 Planarity : 0.004 0.041 1265 Dihedral : 4.514 55.352 1008 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.07 % Allowed : 19.81 % Favored : 76.12 % 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: 0.70 (0.29), residues: 910 helix: 2.14 (0.26), residues: 411 sheet: -1.63 (0.35), residues: 175 loop : -0.42 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 263 HIS 0.002 0.001 HIS B 54 PHE 0.016 0.001 PHE R 34 TYR 0.019 0.001 TYR R 187 ARG 0.005 0.000 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1963.03 seconds wall clock time: 35 minutes 43.33 seconds (2143.33 seconds total)