Starting phenix.real_space_refine on Wed Feb 14 12:08:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vku_32019/02_2024/7vku_32019_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vku_32019/02_2024/7vku_32019.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/7vku_32019/02_2024/7vku_32019.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vku_32019/02_2024/7vku_32019.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vku_32019/02_2024/7vku_32019_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vku_32019/02_2024/7vku_32019_neut.pdb" } 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= -0.000 sd= 0.010 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 39 5.16 5 C 5902 2.51 5 N 1565 2.21 5 O 1713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 43": "OD1" <-> "OD2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ARG 215": "NH1" <-> "NH2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ARG 240": "NH1" <-> "NH2" Residue "C GLU 282": "OE1" <-> "OE2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "X PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 261": "NH1" <-> "NH2" Residue "X GLU 268": "OE1" <-> "OE2" Residue "X GLU 272": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9219 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3314 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 16, 'TRANS': 401} Chain breaks: 2 Chain: "B" Number of atoms: 2460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2460 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 8, 'TRANS': 297} Chain breaks: 2 Chain: "C" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2227 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 6, 'TRANS': 268} Chain breaks: 2 Chain: "X" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1218 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain breaks: 6 Time building chain proxies: 5.24, per 1000 atoms: 0.57 Number of scatterers: 9219 At special positions: 0 Unit cell: (99.6, 95.865, 126.99, 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 39 16.00 O 1713 8.00 N 1565 7.00 C 5902 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.29 Conformation dependent library (CDL) restraints added in 1.7 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 32.6% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.730A pdb=" N ALA A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.647A pdb=" N ASP A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 71 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 434 Processing helix chain 'B' and resid 12 through 16 removed outlier: 3.580A pdb=" N ASP B 16 " --> pdb=" O LYS B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 12 through 16' Processing helix chain 'B' and resid 32 through 40 removed outlier: 3.588A pdb=" N GLN B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'B' and resid 142 through 150 Processing helix chain 'B' and resid 157 through 168 removed outlier: 3.666A pdb=" N MET B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 181 Processing helix chain 'B' and resid 184 through 192 removed outlier: 3.632A pdb=" N GLU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 191 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.587A pdb=" N GLU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.562A pdb=" N SER B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 234 through 240 Processing helix chain 'B' and resid 247 through 272 removed outlier: 3.624A pdb=" N GLN B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 285 through 297 removed outlier: 3.830A pdb=" N SER B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'C' and resid 19 through 31 Processing helix chain 'C' and resid 34 through 38 removed outlier: 4.000A pdb=" N LYS C 38 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 removed outlier: 4.073A pdb=" N LEU C 54 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 84 Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 121 through 130 removed outlier: 4.015A pdb=" N LEU C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 Processing helix chain 'C' and resid 144 through 148 removed outlier: 3.723A pdb=" N LYS C 147 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 148 " --> pdb=" O PHE C 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 144 through 148' Processing helix chain 'C' and resid 156 through 170 removed outlier: 3.548A pdb=" N GLU C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 241 removed outlier: 3.611A pdb=" N LYS C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR C 221 " --> pdb=" O GLN C 217 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 263 removed outlier: 3.596A pdb=" N LEU C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 280 removed outlier: 4.161A pdb=" N ILE C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.904A pdb=" N LEU C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN C 289 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP C 293 " --> pdb=" O ASN C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 324 removed outlier: 4.376A pdb=" N ASN C 321 " --> pdb=" O MET C 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 37 removed outlier: 7.573A pdb=" N VAL A 35 " --> pdb=" O LEU A 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 removed outlier: 3.595A pdb=" N SER A 192 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 180 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 185 " --> pdb=" O ARG A 215 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE A 241 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY A 416 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 443 " --> pdb=" O PHE A 413 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A 480 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 466 Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 42 Processing sheet with id=AA5, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AA6, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.625A pdb=" N LEU C 65 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'X' and resid 210 through 214 removed outlier: 3.713A pdb=" N GLY X 212 " --> pdb=" O LEU X 233 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 244 through 245 Processing sheet with id=AA9, first strand: chain 'X' and resid 302 through 304 382 hydrogen bonds defined for protein. 1074 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: 2.68 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.34: 2951 1.34 - 1.52: 5452 1.52 - 1.71: 935 1.71 - 1.89: 57 1.89 - 2.07: 1 Bond restraints: 9396 Sorted by residual: bond pdb=" C ALA X 264 " pdb=" N ASN X 266 " ideal model delta sigma weight residual 1.332 2.067 -0.735 1.34e-02 5.57e+03 3.01e+03 bond pdb=" CA LEU C 100 " pdb=" C LEU C 100 " ideal model delta sigma weight residual 1.523 1.411 0.112 1.34e-02 5.57e+03 6.99e+01 bond pdb=" CA LYS C 38 " pdb=" C LYS C 38 " ideal model delta sigma weight residual 1.520 1.425 0.095 1.40e-02 5.10e+03 4.59e+01 bond pdb=" CA LEU X 183 " pdb=" C LEU X 183 " ideal model delta sigma weight residual 1.526 1.443 0.082 1.28e-02 6.10e+03 4.13e+01 bond pdb=" C LEU C 100 " pdb=" O LEU C 100 " ideal model delta sigma weight residual 1.235 1.163 0.073 1.26e-02 6.30e+03 3.32e+01 ... (remaining 9391 not shown) Histogram of bond angle deviations from ideal: 92.16 - 100.52: 15 100.52 - 108.89: 807 108.89 - 117.26: 5902 117.26 - 125.63: 5816 125.63 - 134.00: 150 Bond angle restraints: 12690 Sorted by residual: angle pdb=" N LYS C 38 " pdb=" CA LYS C 38 " pdb=" C LYS C 38 " ideal model delta sigma weight residual 114.04 98.35 15.69 1.24e+00 6.50e-01 1.60e+02 angle pdb=" C ALA X 264 " pdb=" N ASN X 266 " pdb=" CA ASN X 266 " ideal model delta sigma weight residual 122.65 108.95 13.70 1.60e+00 3.91e-01 7.33e+01 angle pdb=" N GLY X 195 " pdb=" CA GLY X 195 " pdb=" C GLY X 195 " ideal model delta sigma weight residual 110.69 127.52 -16.83 2.05e+00 2.38e-01 6.74e+01 angle pdb=" O ALA X 264 " pdb=" C ALA X 264 " pdb=" N ASN X 266 " ideal model delta sigma weight residual 122.59 133.04 -10.45 1.33e+00 5.65e-01 6.17e+01 angle pdb=" N LEU X 183 " pdb=" CA LEU X 183 " pdb=" C LEU X 183 " ideal model delta sigma weight residual 107.69 92.16 15.53 2.01e+00 2.48e-01 5.97e+01 ... (remaining 12685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 4869 17.04 - 34.08: 577 34.08 - 51.12: 145 51.12 - 68.15: 19 68.15 - 85.19: 14 Dihedral angle restraints: 5624 sinusoidal: 2270 harmonic: 3354 Sorted by residual: dihedral pdb=" CA LEU B 128 " pdb=" C LEU B 128 " pdb=" N PRO B 129 " pdb=" CA PRO B 129 " ideal model delta harmonic sigma weight residual 180.00 110.04 69.96 0 5.00e+00 4.00e-02 1.96e+02 dihedral pdb=" N VAL X 178 " pdb=" C VAL X 178 " pdb=" CA VAL X 178 " pdb=" CB VAL X 178 " ideal model delta harmonic sigma weight residual 123.40 148.29 -24.89 0 2.50e+00 1.60e-01 9.92e+01 dihedral pdb=" CA LEU C 60 " pdb=" C LEU C 60 " pdb=" N PRO C 61 " pdb=" CA PRO C 61 " ideal model delta harmonic sigma weight residual 180.00 132.37 47.63 0 5.00e+00 4.00e-02 9.07e+01 ... (remaining 5621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.193: 1429 0.193 - 0.387: 12 0.387 - 0.580: 2 0.580 - 0.774: 1 0.774 - 0.967: 2 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CA VAL X 178 " pdb=" N VAL X 178 " pdb=" C VAL X 178 " pdb=" CB VAL X 178 " both_signs ideal model delta sigma weight residual False 2.44 1.47 0.97 2.00e-01 2.50e+01 2.34e+01 chirality pdb=" CA PHE B 18 " pdb=" N PHE B 18 " pdb=" C PHE B 18 " pdb=" CB PHE B 18 " both_signs ideal model delta sigma weight residual False 2.51 1.60 0.91 2.00e-01 2.50e+01 2.08e+01 chirality pdb=" CA ASP C 99 " pdb=" N ASP C 99 " pdb=" C ASP C 99 " pdb=" CB ASP C 99 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.66 2.00e-01 2.50e+01 1.07e+01 ... (remaining 1443 not shown) Planarity restraints: 1599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 60 " -0.083 5.00e-02 4.00e+02 1.23e-01 2.43e+01 pdb=" N PRO C 61 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 128 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO B 129 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 450 " 0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO A 451 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 451 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 451 " 0.046 5.00e-02 4.00e+02 ... (remaining 1596 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 9 2.27 - 2.93: 3856 2.93 - 3.58: 12279 3.58 - 4.24: 20972 4.24 - 4.90: 36134 Nonbonded interactions: 73250 Sorted by model distance: nonbonded pdb=" CE1 PHE X 187 " pdb=" O GLU X 192 " model vdw 1.611 3.340 nonbonded pdb=" CD1 PHE X 187 " pdb=" O GLU X 192 " model vdw 1.724 3.340 nonbonded pdb=" O VAL X 263 " pdb=" O VAL X 267 " model vdw 1.760 3.040 nonbonded pdb=" CE1 TYR X 79 " pdb=" NH2 ARG X 235 " model vdw 2.059 3.420 nonbonded pdb=" N GLU C 98 " pdb=" OE1 GLU C 98 " model vdw 2.156 2.520 ... (remaining 73245 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 2.180 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.260 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.013 0.735 9396 Z= 0.740 Angle : 1.238 16.828 12690 Z= 0.708 Chirality : 0.076 0.967 1446 Planarity : 0.008 0.123 1599 Dihedral : 16.096 85.193 3450 Min Nonbonded Distance : 1.611 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.71 % Allowed : 10.09 % Favored : 89.20 % Rotamer: Outliers : 2.23 % Allowed : 10.55 % Favored : 87.22 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.27 % 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: -5.75 (0.19), residues: 1120 helix: -4.25 (0.12), residues: 377 sheet: -3.34 (0.24), residues: 310 loop : -3.44 (0.25), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 246 HIS 0.011 0.002 HIS A 78 PHE 0.028 0.003 PHE B 68 TYR 0.025 0.003 TYR X 314 ARG 0.015 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.5822 (ptt) cc_final: 0.5545 (ptt) outliers start: 23 outliers final: 11 residues processed: 167 average time/residue: 0.2218 time to fit residues: 50.8561 Evaluate side-chains 114 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain X residue 94 MET Chi-restraints excluded: chain X residue 183 LEU Chi-restraints excluded: chain X residue 218 SER Chi-restraints excluded: chain X residue 220 THR Chi-restraints excluded: chain X residue 301 THR Chi-restraints excluded: chain X residue 353 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 77 GLN A 78 HIS A 83 ASN A 135 ASN A 175 ASN A 193 GLN A 207 GLN A 254 GLN A 303 ASN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN A 466 HIS B 94 ASN B 242 GLN B 249 HIS B 256 GLN B 321 GLN C 7 HIS C 269 ASN C 277 GLN X 95 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9396 Z= 0.175 Angle : 0.669 13.414 12690 Z= 0.347 Chirality : 0.042 0.193 1446 Planarity : 0.006 0.087 1599 Dihedral : 6.814 58.871 1246 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.00 % Favored : 90.73 % Rotamer: Outliers : 1.94 % Allowed : 15.88 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.27 % 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: -4.03 (0.22), residues: 1122 helix: -1.96 (0.22), residues: 389 sheet: -2.66 (0.26), residues: 295 loop : -3.18 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 260 HIS 0.004 0.001 HIS B 248 PHE 0.012 0.001 PHE B 18 TYR 0.010 0.001 TYR B 163 ARG 0.005 0.000 ARG X 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.7470 (mttm) cc_final: 0.7212 (mtmm) REVERT: A 156 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7998 (p) REVERT: A 157 ARG cc_start: 0.7355 (ttp80) cc_final: 0.7097 (ttp80) REVERT: A 291 MET cc_start: 0.7651 (mmm) cc_final: 0.7147 (tpt) REVERT: B 162 MET cc_start: 0.8362 (mmt) cc_final: 0.7994 (mmp) REVERT: C 155 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.6281 (m-80) outliers start: 20 outliers final: 11 residues processed: 137 average time/residue: 0.2069 time to fit residues: 39.9598 Evaluate side-chains 121 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain X residue 80 PHE Chi-restraints excluded: chain X residue 183 LEU Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 200 SER Chi-restraints excluded: chain X residue 230 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 28 optimal weight: 0.0570 chunk 102 optimal weight: 4.9990 chunk 111 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN B 249 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9396 Z= 0.175 Angle : 0.628 12.311 12690 Z= 0.321 Chirality : 0.042 0.175 1446 Planarity : 0.005 0.091 1599 Dihedral : 6.093 54.941 1231 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.00 % Favored : 90.73 % Rotamer: Outliers : 2.03 % Allowed : 17.72 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.24), residues: 1122 helix: -0.55 (0.26), residues: 390 sheet: -2.28 (0.28), residues: 288 loop : -3.04 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP X 260 HIS 0.008 0.001 HIS B 249 PHE 0.017 0.001 PHE A 237 TYR 0.009 0.001 TYR X 314 ARG 0.002 0.000 ARG C 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.7553 (mttm) cc_final: 0.7318 (mtmm) REVERT: A 156 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7901 (p) REVERT: B 162 MET cc_start: 0.8414 (mmt) cc_final: 0.7945 (mmp) REVERT: C 155 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.6417 (m-80) REVERT: X 80 PHE cc_start: 0.5986 (OUTLIER) cc_final: 0.5165 (p90) REVERT: X 183 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6390 (tt) outliers start: 21 outliers final: 9 residues processed: 136 average time/residue: 0.1962 time to fit residues: 38.3787 Evaluate side-chains 116 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain X residue 80 PHE Chi-restraints excluded: chain X residue 183 LEU Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 200 SER Chi-restraints excluded: chain X residue 349 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 29 optimal weight: 0.2980 chunk 90 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 GLN B 112 ASN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS C 67 ASN C 156 ASN C 224 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9396 Z= 0.158 Angle : 0.605 11.258 12690 Z= 0.309 Chirality : 0.042 0.162 1446 Planarity : 0.005 0.084 1599 Dihedral : 5.723 51.611 1228 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.82 % Favored : 90.91 % Rotamer: Outliers : 2.81 % Allowed : 17.13 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.24), residues: 1122 helix: 0.07 (0.27), residues: 391 sheet: -2.08 (0.28), residues: 291 loop : -2.98 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP X 260 HIS 0.010 0.001 HIS B 249 PHE 0.015 0.001 PHE A 237 TYR 0.009 0.001 TYR X 314 ARG 0.004 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7769 (p) REVERT: B 26 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7124 (mt0) REVERT: B 162 MET cc_start: 0.8468 (mmt) cc_final: 0.7986 (mmp) REVERT: C 155 TYR cc_start: 0.7310 (OUTLIER) cc_final: 0.6894 (m-80) REVERT: X 80 PHE cc_start: 0.6041 (OUTLIER) cc_final: 0.5237 (p90) REVERT: X 183 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6457 (tt) outliers start: 29 outliers final: 15 residues processed: 134 average time/residue: 0.1907 time to fit residues: 36.8013 Evaluate side-chains 125 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain C residue 155 TYR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain X residue 80 PHE Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 183 LEU Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 200 SER Chi-restraints excluded: chain X residue 349 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9396 Z= 0.200 Angle : 0.603 9.473 12690 Z= 0.310 Chirality : 0.042 0.153 1446 Planarity : 0.005 0.087 1599 Dihedral : 5.655 52.240 1228 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.91 % Favored : 90.91 % Rotamer: Outliers : 2.71 % Allowed : 19.07 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.25), residues: 1122 helix: 0.41 (0.27), residues: 394 sheet: -1.98 (0.28), residues: 301 loop : -3.01 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP X 260 HIS 0.010 0.001 HIS B 249 PHE 0.014 0.001 PHE A 237 TYR 0.010 0.001 TYR X 314 ARG 0.005 0.000 ARG X 235 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8197 (mtmm) cc_final: 0.7907 (mtmm) REVERT: A 156 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7933 (p) REVERT: B 162 MET cc_start: 0.8496 (mmt) cc_final: 0.8024 (mmp) REVERT: X 80 PHE cc_start: 0.6197 (OUTLIER) cc_final: 0.5533 (p90) REVERT: X 183 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6711 (tt) outliers start: 28 outliers final: 18 residues processed: 127 average time/residue: 0.2067 time to fit residues: 37.3007 Evaluate side-chains 124 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain X residue 80 PHE Chi-restraints excluded: chain X residue 183 LEU Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 200 SER Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 349 ASN Chi-restraints excluded: chain X residue 353 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 90 optimal weight: 0.0000 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.0570 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.1906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9396 Z= 0.212 Angle : 0.604 8.427 12690 Z= 0.310 Chirality : 0.042 0.146 1446 Planarity : 0.005 0.083 1599 Dihedral : 5.598 52.250 1228 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.09 % Favored : 90.73 % Rotamer: Outliers : 2.81 % Allowed : 19.65 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.25), residues: 1122 helix: 0.65 (0.28), residues: 394 sheet: -1.89 (0.28), residues: 305 loop : -2.97 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP X 260 HIS 0.010 0.001 HIS B 249 PHE 0.014 0.001 PHE A 237 TYR 0.010 0.001 TYR X 314 ARG 0.003 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7852 (mtmm) REVERT: A 121 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7271 (mmtt) REVERT: A 156 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7975 (p) REVERT: B 26 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7323 (mt0) REVERT: B 162 MET cc_start: 0.8507 (mmt) cc_final: 0.8037 (mmp) REVERT: X 80 PHE cc_start: 0.6220 (OUTLIER) cc_final: 0.5803 (p90) outliers start: 29 outliers final: 19 residues processed: 131 average time/residue: 0.2153 time to fit residues: 39.9456 Evaluate side-chains 129 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain X residue 80 PHE Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 198 VAL Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 349 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 108 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9396 Z= 0.151 Angle : 0.592 8.499 12690 Z= 0.302 Chirality : 0.041 0.169 1446 Planarity : 0.005 0.079 1599 Dihedral : 5.329 50.169 1226 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.82 % Favored : 91.00 % Rotamer: Outliers : 3.19 % Allowed : 19.85 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.25), residues: 1122 helix: 0.91 (0.28), residues: 392 sheet: -1.81 (0.28), residues: 307 loop : -2.84 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP X 260 HIS 0.005 0.001 HIS B 248 PHE 0.014 0.001 PHE A 237 TYR 0.009 0.001 TYR X 314 ARG 0.003 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8135 (mtmm) cc_final: 0.7846 (mtmm) REVERT: A 156 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7924 (p) REVERT: B 26 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7127 (mt0) REVERT: B 162 MET cc_start: 0.8531 (mmt) cc_final: 0.8188 (mmp) REVERT: X 80 PHE cc_start: 0.6401 (OUTLIER) cc_final: 0.6178 (p90) REVERT: X 90 LYS cc_start: 0.7721 (tmmt) cc_final: 0.7418 (ttpt) outliers start: 33 outliers final: 20 residues processed: 137 average time/residue: 0.2049 time to fit residues: 39.8554 Evaluate side-chains 131 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain X residue 80 PHE Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 332 VAL Chi-restraints excluded: chain X residue 349 ASN Chi-restraints excluded: chain X residue 353 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 ASN A 450 HIS ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 9396 Z= 0.420 Angle : 0.707 8.276 12690 Z= 0.362 Chirality : 0.046 0.175 1446 Planarity : 0.005 0.089 1599 Dihedral : 5.751 57.651 1226 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.27 % Favored : 90.46 % Rotamer: Outliers : 2.61 % Allowed : 20.91 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.25), residues: 1122 helix: 0.73 (0.28), residues: 389 sheet: -1.88 (0.28), residues: 320 loop : -2.89 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP X 260 HIS 0.006 0.001 HIS A 422 PHE 0.020 0.002 PHE B 18 TYR 0.016 0.002 TYR X 314 ARG 0.004 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8115 (mtmm) cc_final: 0.7878 (mtmm) REVERT: A 156 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8195 (p) REVERT: B 162 MET cc_start: 0.8613 (mmt) cc_final: 0.8150 (mmp) REVERT: X 80 PHE cc_start: 0.6368 (OUTLIER) cc_final: 0.6127 (p90) outliers start: 27 outliers final: 17 residues processed: 126 average time/residue: 0.1955 time to fit residues: 35.5872 Evaluate side-chains 119 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain X residue 80 PHE Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 349 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 8.9990 chunk 104 optimal weight: 20.0000 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 0.0020 chunk 107 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 133 ASN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 ASN B 101 HIS ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 250 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9396 Z= 0.151 Angle : 0.607 9.370 12690 Z= 0.309 Chirality : 0.042 0.152 1446 Planarity : 0.005 0.077 1599 Dihedral : 5.414 51.020 1226 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.82 % Favored : 91.00 % Rotamer: Outliers : 2.71 % Allowed : 21.10 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.26), residues: 1122 helix: 1.08 (0.28), residues: 391 sheet: -1.75 (0.28), residues: 305 loop : -2.83 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP X 260 HIS 0.004 0.001 HIS A 310 PHE 0.014 0.001 PHE A 477 TYR 0.010 0.001 TYR X 314 ARG 0.005 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8056 (mtmm) cc_final: 0.7728 (mtmm) REVERT: A 156 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.8048 (p) REVERT: B 26 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7428 (mt0) REVERT: B 162 MET cc_start: 0.8524 (mmt) cc_final: 0.8050 (mmp) REVERT: X 80 PHE cc_start: 0.6254 (OUTLIER) cc_final: 0.6018 (p90) outliers start: 28 outliers final: 20 residues processed: 126 average time/residue: 0.2052 time to fit residues: 37.5265 Evaluate side-chains 123 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain X residue 80 PHE Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 349 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 9 optimal weight: 0.0000 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 133 ASN ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 ASN ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9396 Z= 0.266 Angle : 0.639 9.987 12690 Z= 0.326 Chirality : 0.043 0.147 1446 Planarity : 0.005 0.084 1599 Dihedral : 5.497 53.390 1226 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.00 % Favored : 90.82 % Rotamer: Outliers : 2.32 % Allowed : 21.88 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.26), residues: 1122 helix: 1.13 (0.28), residues: 390 sheet: -1.81 (0.28), residues: 321 loop : -2.79 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP X 260 HIS 0.005 0.001 HIS A 78 PHE 0.013 0.002 PHE A 477 TYR 0.013 0.001 TYR X 314 ARG 0.004 0.000 ARG A 157 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8039 (mtmm) cc_final: 0.7705 (mtmm) REVERT: A 156 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8099 (p) REVERT: B 162 MET cc_start: 0.8569 (mmt) cc_final: 0.8100 (mmp) outliers start: 24 outliers final: 21 residues processed: 118 average time/residue: 0.1938 time to fit residues: 33.1462 Evaluate side-chains 120 residues out of total 1033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain X residue 93 SER Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 349 ASN Chi-restraints excluded: chain X residue 353 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.136489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.096756 restraints weight = 14197.880| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.43 r_work: 0.3082 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9396 Z= 0.224 Angle : 0.622 10.133 12690 Z= 0.318 Chirality : 0.042 0.144 1446 Planarity : 0.005 0.080 1599 Dihedral : 5.459 52.488 1226 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.09 % Favored : 90.73 % Rotamer: Outliers : 2.71 % Allowed : 21.59 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.26), residues: 1122 helix: 1.23 (0.28), residues: 390 sheet: -1.78 (0.29), residues: 303 loop : -2.73 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP X 260 HIS 0.004 0.001 HIS B 248 PHE 0.014 0.001 PHE A 477 TYR 0.012 0.001 TYR X 314 ARG 0.004 0.000 ARG A 157 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2163.07 seconds wall clock time: 39 minutes 53.38 seconds (2393.38 seconds total)