Starting phenix.real_space_refine on Wed Feb 14 10:14:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un6_26614/02_2024/7un6_26614.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un6_26614/02_2024/7un6_26614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un6_26614/02_2024/7un6_26614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un6_26614/02_2024/7un6_26614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un6_26614/02_2024/7un6_26614.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un6_26614/02_2024/7un6_26614.pdb" } resolution = 3.3 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= 0.068 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 5808 2.51 5 N 1533 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 64": "OD1" <-> "OD2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "A GLU 933": "OE1" <-> "OE2" Residue "A TYR 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1282": "OE1" <-> "OE2" Residue "B TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 9042 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5186 Classifications: {'peptide': 648} Link IDs: {'PCIS': 3, 'PTRANS': 34, 'TRANS': 610} Chain breaks: 8 Chain: "B" Number of atoms: 1965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1965 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 13, 'TRANS': 226} Chain breaks: 1 Chain: "C" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1891 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 11, 'TRANS': 218} Chain breaks: 2 Time building chain proxies: 5.12, per 1000 atoms: 0.57 Number of scatterers: 9042 At special positions: 0 Unit cell: (90.75, 131.175, 135.3, 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 1660 8.00 N 1533 7.00 C 5808 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: 3.40 Conformation dependent library (CDL) restraints added in 1.7 seconds 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 31.8% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 271 through 275 removed outlier: 4.091A pdb=" N SER A 275 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 removed outlier: 4.179A pdb=" N GLY A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 343 Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 950 through 968 Processing helix chain 'A' and resid 1060 through 1071 Processing helix chain 'A' and resid 1083 through 1088 Processing helix chain 'A' and resid 1090 through 1118 removed outlier: 3.535A pdb=" N ARG A1117 " --> pdb=" O THR A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1146 removed outlier: 3.751A pdb=" N ARG A1128 " --> pdb=" O GLU A1124 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR A1133 " --> pdb=" O GLN A1129 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TRP A1136 " --> pdb=" O SER A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1283 Processing helix chain 'B' and resid 74 through 122 Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 169 through 178 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 189 through 194 Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 313 through 333 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.655A pdb=" N TYR B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 123 Proline residue: C 112 - end of helix Processing helix chain 'C' and resid 169 through 177 Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 296 through 302 Processing helix chain 'C' and resid 316 through 333 Processing helix chain 'C' and resid 337 through 343 Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.272A pdb=" N LEU A 65 " --> pdb=" O GLU A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 188 removed outlier: 6.668A pdb=" N ILE A 183 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU A 177 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N TYR A 185 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL A 175 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP A 556 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N VAL A 169 " --> pdb=" O SER A 554 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER A 554 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE A 171 " --> pdb=" O MET A 552 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N MET A 552 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS A 173 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR A 550 " --> pdb=" O CYS A 173 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 175 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL A 548 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU A 177 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 546 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 557 " --> pdb=" O CYS A 566 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N CYS A 566 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TRP A 559 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL A 564 " --> pdb=" O TRP A 559 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 356 removed outlier: 6.662A pdb=" N VAL A 546 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU A 177 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL A 548 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 175 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR A 550 " --> pdb=" O CYS A 173 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS A 173 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N MET A 552 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE A 171 " --> pdb=" O MET A 552 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER A 554 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N VAL A 169 " --> pdb=" O SER A 554 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP A 556 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 269 removed outlier: 6.753A pdb=" N GLU A 297 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LYS A 223 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL A 299 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A 221 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL A 301 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLN A 219 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 215 " --> pdb=" O LYS A 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 280 removed outlier: 5.963A pdb=" N TRP A 278 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N SER A 231 " --> pdb=" O TRP A 278 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 215 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLN A 219 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL A 301 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A 221 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N VAL A 299 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LYS A 223 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU A 297 " --> pdb=" O LYS A 223 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 291 through 306 current: chain 'A' and resid 337 through 338 Processing sheet with id=AA6, first strand: chain 'A' and resid 631 through 635 removed outlier: 6.530A pdb=" N TRP A 621 " --> pdb=" O ILE A 634 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 631 through 635 removed outlier: 6.530A pdb=" N TRP A 621 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR A 616 " --> pdb=" O ASP A 611 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 609 " --> pdb=" O MET A 618 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LYS A 620 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL A 607 " --> pdb=" O LYS A 620 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N PHE A 622 " --> pdb=" O GLY A 605 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY A 605 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LEU A 624 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL A 603 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N VAL A 603 " --> pdb=" O ASP A 592 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP A 592 " --> pdb=" O VAL A 603 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 680 through 681 Processing sheet with id=AA9, first strand: chain 'A' and resid 931 through 932 removed outlier: 3.873A pdb=" N PHE A 978 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU A 984 " --> pdb=" O PHE A 978 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLY A 991 " --> pdb=" O GLY A1000 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLY A1000 " --> pdb=" O GLY A 991 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 196 through 203 removed outlier: 4.035A pdb=" N LEU B 214 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS B 231 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG B 234 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY B 254 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ARG B 236 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE B 252 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 270 through 278 Processing sheet with id=AB3, first strand: chain 'C' and resid 199 through 203 Processing sheet with id=AB4, first strand: chain 'C' and resid 233 through 235 removed outlier: 5.790A pdb=" N ARG C 234 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 270 through 278 353 hydrogen bonds defined for protein. 990 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: 2.58 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2928 1.34 - 1.46: 1983 1.46 - 1.58: 4281 1.58 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 9253 Sorted by residual: bond pdb=" C PHE A 584 " pdb=" N CYS A 585 " ideal model delta sigma weight residual 1.329 1.248 0.081 1.86e-02 2.89e+03 1.87e+01 bond pdb=" CG LEU C 81 " pdb=" CD2 LEU C 81 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.30e+00 bond pdb=" CB VAL C 201 " pdb=" CG2 VAL C 201 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.99e-01 bond pdb=" CB GLU A1081 " pdb=" CG GLU A1081 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.93e-01 bond pdb=" CB ILE B 192 " pdb=" CG1 ILE B 192 " ideal model delta sigma weight residual 1.530 1.512 0.018 2.00e-02 2.50e+03 8.33e-01 ... (remaining 9248 not shown) Histogram of bond angle deviations from ideal: 97.58 - 104.86: 179 104.86 - 112.14: 4562 112.14 - 119.42: 3105 119.42 - 126.70: 4524 126.70 - 133.98: 140 Bond angle restraints: 12510 Sorted by residual: angle pdb=" N GLU A 691 " pdb=" CA GLU A 691 " pdb=" C GLU A 691 " ideal model delta sigma weight residual 111.07 115.58 -4.51 1.07e+00 8.73e-01 1.78e+01 angle pdb=" CA GLU A1081 " pdb=" CB GLU A1081 " pdb=" CG GLU A1081 " ideal model delta sigma weight residual 114.10 121.36 -7.26 2.00e+00 2.50e-01 1.32e+01 angle pdb=" N GLN B 111 " pdb=" CA GLN B 111 " pdb=" C GLN B 111 " ideal model delta sigma weight residual 113.77 109.79 3.98 1.32e+00 5.74e-01 9.09e+00 angle pdb=" N VAL A 692 " pdb=" CA VAL A 692 " pdb=" C VAL A 692 " ideal model delta sigma weight residual 107.75 111.45 -3.70 1.46e+00 4.69e-01 6.41e+00 angle pdb=" C ILE A 973 " pdb=" N MET A 974 " pdb=" CA MET A 974 " ideal model delta sigma weight residual 121.80 117.67 4.13 1.71e+00 3.42e-01 5.82e+00 ... (remaining 12505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 5060 17.81 - 35.62: 413 35.62 - 53.43: 61 53.43 - 71.24: 17 71.24 - 89.05: 14 Dihedral angle restraints: 5565 sinusoidal: 2315 harmonic: 3250 Sorted by residual: dihedral pdb=" CA GLU A 691 " pdb=" C GLU A 691 " pdb=" N VAL A 692 " pdb=" CA VAL A 692 " ideal model delta harmonic sigma weight residual -180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ASN C 221 " pdb=" C ASN C 221 " pdb=" N GLU C 222 " pdb=" CA GLU C 222 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ILE A 973 " pdb=" C ILE A 973 " pdb=" N MET A 974 " pdb=" CA MET A 974 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 5562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 979 0.039 - 0.078: 263 0.078 - 0.117: 103 0.117 - 0.156: 24 0.156 - 0.195: 1 Chirality restraints: 1370 Sorted by residual: chirality pdb=" CB ILE B 192 " pdb=" CA ILE B 192 " pdb=" CG1 ILE B 192 " pdb=" CG2 ILE B 192 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.54e-01 chirality pdb=" CA PHE C 216 " pdb=" N PHE C 216 " pdb=" C PHE C 216 " pdb=" CB PHE C 216 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA ILE B 199 " pdb=" N ILE B 199 " pdb=" C ILE B 199 " pdb=" CB ILE B 199 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 1367 not shown) Planarity restraints: 1608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 154 " -0.177 9.50e-02 1.11e+02 7.93e-02 4.03e+00 pdb=" NE ARG A 154 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 154 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 154 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 154 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 111 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO B 112 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 622 " 0.009 2.00e-02 2.50e+03 1.06e-02 1.97e+00 pdb=" CG PHE A 622 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 622 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 622 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 622 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 622 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 622 " 0.001 2.00e-02 2.50e+03 ... (remaining 1605 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 50 2.48 - 3.09: 6799 3.09 - 3.69: 13564 3.69 - 4.30: 19819 4.30 - 4.90: 32624 Nonbonded interactions: 72856 Sorted by model distance: nonbonded pdb=" OH TYR C 233 " pdb=" OD1 ASP C 323 " model vdw 1.879 2.440 nonbonded pdb=" OG SER A 287 " pdb=" OD2 ASP C 248 " model vdw 1.955 2.440 nonbonded pdb=" OH TYR A 997 " pdb=" O LEU A1029 " model vdw 1.985 2.440 nonbonded pdb=" OH TYR A 70 " pdb=" OE1 GLU A 129 " model vdw 2.082 2.440 nonbonded pdb=" OH TYR B 233 " pdb=" OD1 ASP B 323 " model vdw 2.126 2.440 ... (remaining 72851 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 73 through 126 or resid 166 through 306 or resid 315 throu \ gh 349)) selection = chain 'C' } 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.480 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.540 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5485 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 0.081 9253 Z= 0.243 Angle : 0.600 7.257 12510 Z= 0.331 Chirality : 0.044 0.195 1370 Planarity : 0.004 0.079 1608 Dihedral : 13.875 89.046 3455 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.89 (0.25), residues: 1090 helix: 0.66 (0.30), residues: 293 sheet: -1.50 (0.32), residues: 218 loop : -0.80 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 209 HIS 0.004 0.001 HIS A 577 PHE 0.024 0.002 PHE A 622 TYR 0.018 0.001 TYR A1034 ARG 0.007 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 185 TYR cc_start: 0.4564 (t80) cc_final: 0.3850 (p90) REVERT: A 193 GLN cc_start: 0.6544 (mm110) cc_final: 0.6295 (mt0) REVERT: A 206 TYR cc_start: 0.5558 (t80) cc_final: 0.5086 (t80) REVERT: A 616 THR cc_start: 0.7799 (p) cc_final: 0.7590 (t) REVERT: B 94 LYS cc_start: 0.6343 (mttp) cc_final: 0.5796 (mmtm) REVERT: B 117 ARG cc_start: 0.6195 (ttp-170) cc_final: 0.3046 (tmm160) REVERT: B 202 LYS cc_start: 0.6898 (mttm) cc_final: 0.6518 (mmmt) REVERT: B 332 GLU cc_start: 0.5227 (pt0) cc_final: 0.5007 (pt0) REVERT: B 337 ARG cc_start: 0.6925 (mtp180) cc_final: 0.6220 (mtt-85) REVERT: C 76 ARG cc_start: 0.6178 (ttm170) cc_final: 0.5442 (tpt170) REVERT: C 202 LYS cc_start: 0.6848 (mtpp) cc_final: 0.6250 (mmtt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2434 time to fit residues: 60.6127 Evaluate side-chains 116 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 346 GLN A1101 ASN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 HIS C 111 GLN C 221 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5642 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9253 Z= 0.279 Angle : 0.669 7.980 12510 Z= 0.344 Chirality : 0.046 0.186 1370 Planarity : 0.005 0.068 1608 Dihedral : 5.178 27.194 1201 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.69 % Allowed : 8.73 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.65 (0.25), residues: 1090 helix: 0.69 (0.29), residues: 293 sheet: -1.31 (0.32), residues: 219 loop : -0.58 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 171 HIS 0.006 0.001 HIS A 706 PHE 0.036 0.002 PHE C 212 TYR 0.016 0.002 TYR A1002 ARG 0.004 0.000 ARG C 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 LEU cc_start: 0.6838 (mt) cc_final: 0.6548 (tp) REVERT: A 193 GLN cc_start: 0.6847 (mm110) cc_final: 0.6641 (mt0) REVERT: A 558 MET cc_start: 0.8046 (ttt) cc_final: 0.7806 (ttp) REVERT: B 337 ARG cc_start: 0.6981 (mtp180) cc_final: 0.6168 (mtt-85) REVERT: C 76 ARG cc_start: 0.6152 (ttm170) cc_final: 0.5343 (tpt170) REVERT: C 170 PHE cc_start: 0.5349 (t80) cc_final: 0.5107 (t80) REVERT: C 202 LYS cc_start: 0.6333 (mtpp) cc_final: 0.5780 (mptt) REVERT: C 216 PHE cc_start: 0.6138 (OUTLIER) cc_final: 0.5753 (m-10) outliers start: 17 outliers final: 8 residues processed: 129 average time/residue: 0.1708 time to fit residues: 32.8596 Evaluate side-chains 115 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain C residue 216 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 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 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5645 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9253 Z= 0.223 Angle : 0.589 7.193 12510 Z= 0.303 Chirality : 0.044 0.165 1370 Planarity : 0.004 0.061 1608 Dihedral : 4.912 23.743 1201 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.79 % Allowed : 11.41 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.44 (0.25), residues: 1090 helix: 0.69 (0.29), residues: 301 sheet: -1.26 (0.32), residues: 207 loop : -0.34 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 171 HIS 0.006 0.001 HIS C 328 PHE 0.040 0.002 PHE C 212 TYR 0.019 0.002 TYR A 206 ARG 0.003 0.000 ARG A 569 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 TYR cc_start: 0.6422 (t80) cc_final: 0.4231 (p90) REVERT: A 193 GLN cc_start: 0.6841 (mm110) cc_final: 0.6638 (mt0) REVERT: A 623 LYS cc_start: 0.8351 (ptpt) cc_final: 0.8071 (ptpp) REVERT: B 328 HIS cc_start: 0.5726 (t70) cc_final: 0.5250 (t-90) REVERT: B 337 ARG cc_start: 0.6951 (mtp180) cc_final: 0.6163 (mtt-85) REVERT: C 76 ARG cc_start: 0.6252 (ttm170) cc_final: 0.5327 (tpt170) REVERT: C 170 PHE cc_start: 0.5338 (t80) cc_final: 0.5110 (t80) REVERT: C 202 LYS cc_start: 0.6207 (mtpp) cc_final: 0.5635 (mmtt) outliers start: 18 outliers final: 13 residues processed: 129 average time/residue: 0.1759 time to fit residues: 33.9139 Evaluate side-chains 122 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 216 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 60 optimal weight: 20.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5679 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9253 Z= 0.230 Angle : 0.580 7.210 12510 Z= 0.298 Chirality : 0.044 0.163 1370 Planarity : 0.004 0.055 1608 Dihedral : 4.816 21.751 1201 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.48 % Allowed : 12.50 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.18 (0.25), residues: 1090 helix: 0.85 (0.30), residues: 295 sheet: -0.99 (0.33), residues: 205 loop : -0.19 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1136 HIS 0.012 0.001 HIS A 83 PHE 0.043 0.002 PHE C 212 TYR 0.012 0.001 TYR C 223 ARG 0.004 0.000 ARG A1141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7925 (mp) REVERT: A 185 TYR cc_start: 0.6298 (t80) cc_final: 0.4275 (p90) REVERT: A 193 GLN cc_start: 0.6831 (mm110) cc_final: 0.6628 (mt0) REVERT: A 561 ASP cc_start: 0.7738 (p0) cc_final: 0.7339 (p0) REVERT: A 623 LYS cc_start: 0.8301 (ptpt) cc_final: 0.8028 (ptpp) REVERT: B 328 HIS cc_start: 0.5664 (t70) cc_final: 0.5450 (t70) REVERT: C 76 ARG cc_start: 0.6373 (ttm170) cc_final: 0.5351 (tpt170) REVERT: C 202 LYS cc_start: 0.6143 (mtpp) cc_final: 0.5619 (mptt) REVERT: C 253 MET cc_start: 0.5510 (mmm) cc_final: 0.4212 (ptp) outliers start: 25 outliers final: 20 residues processed: 133 average time/residue: 0.1962 time to fit residues: 38.3045 Evaluate side-chains 127 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 217 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 44 optimal weight: 0.0670 chunk 91 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 21 optimal weight: 0.0980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5653 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9253 Z= 0.187 Angle : 0.548 7.811 12510 Z= 0.280 Chirality : 0.043 0.157 1370 Planarity : 0.004 0.046 1608 Dihedral : 4.661 21.841 1201 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.88 % Allowed : 13.69 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.04 (0.25), residues: 1090 helix: 0.93 (0.30), residues: 295 sheet: -0.77 (0.33), residues: 208 loop : -0.13 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 171 HIS 0.007 0.001 HIS C 328 PHE 0.036 0.002 PHE C 212 TYR 0.013 0.001 TYR A 206 ARG 0.002 0.000 ARG A 569 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 185 TYR cc_start: 0.6108 (t80) cc_final: 0.4244 (p90) REVERT: A 561 ASP cc_start: 0.7629 (p0) cc_final: 0.7225 (p0) REVERT: A 623 LYS cc_start: 0.8247 (ptpt) cc_final: 0.7979 (ptpp) REVERT: A 929 PHE cc_start: 0.5459 (t80) cc_final: 0.4510 (t80) REVERT: B 179 ASP cc_start: 0.6875 (m-30) cc_final: 0.6340 (t0) REVERT: C 76 ARG cc_start: 0.6374 (ttm170) cc_final: 0.5309 (tpt170) REVERT: C 202 LYS cc_start: 0.6166 (mtpp) cc_final: 0.5560 (mmtt) REVERT: C 224 PHE cc_start: 0.3336 (OUTLIER) cc_final: 0.2122 (p90) REVERT: C 253 MET cc_start: 0.5490 (mmm) cc_final: 0.4207 (ptp) outliers start: 29 outliers final: 23 residues processed: 139 average time/residue: 0.2016 time to fit residues: 39.8537 Evaluate side-chains 133 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 217 HIS Chi-restraints excluded: chain C residue 224 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 0.0770 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 0.0870 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5645 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9253 Z= 0.179 Angle : 0.541 7.433 12510 Z= 0.277 Chirality : 0.043 0.153 1370 Planarity : 0.004 0.046 1608 Dihedral : 4.575 22.625 1201 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.37 % Allowed : 13.89 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.02 (0.25), residues: 1090 helix: 0.95 (0.30), residues: 295 sheet: -0.72 (0.33), residues: 206 loop : -0.08 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1136 HIS 0.007 0.001 HIS C 328 PHE 0.042 0.002 PHE C 212 TYR 0.011 0.001 TYR B 223 ARG 0.003 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 112 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 TYR cc_start: 0.6075 (t80) cc_final: 0.4256 (p90) REVERT: A 193 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6681 (mt0) REVERT: A 304 LEU cc_start: 0.5812 (OUTLIER) cc_final: 0.5578 (pp) REVERT: A 561 ASP cc_start: 0.7576 (p0) cc_final: 0.7213 (p0) REVERT: A 623 LYS cc_start: 0.8197 (ptpt) cc_final: 0.7918 (ptpp) REVERT: B 179 ASP cc_start: 0.6856 (m-30) cc_final: 0.6325 (t0) REVERT: C 76 ARG cc_start: 0.6355 (ttm170) cc_final: 0.5250 (tpt170) REVERT: C 202 LYS cc_start: 0.6150 (mtpp) cc_final: 0.5584 (mptt) REVERT: C 224 PHE cc_start: 0.3036 (OUTLIER) cc_final: 0.1763 (p90) REVERT: C 253 MET cc_start: 0.5502 (mmm) cc_final: 0.4260 (ptp) outliers start: 34 outliers final: 25 residues processed: 136 average time/residue: 0.1869 time to fit residues: 37.2762 Evaluate side-chains 136 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 217 HIS Chi-restraints excluded: chain C residue 221 ASN Chi-restraints excluded: chain C residue 224 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 155 HIS A 170 ASN A 577 HIS B 188 HIS B 226 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5742 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9253 Z= 0.325 Angle : 0.615 7.617 12510 Z= 0.317 Chirality : 0.046 0.173 1370 Planarity : 0.004 0.045 1608 Dihedral : 4.858 22.870 1201 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.67 % Allowed : 13.99 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.20 (0.25), residues: 1090 helix: 0.73 (0.30), residues: 294 sheet: -0.86 (0.34), residues: 211 loop : -0.18 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 278 HIS 0.011 0.002 HIS A 83 PHE 0.043 0.002 PHE C 212 TYR 0.014 0.002 TYR C 223 ARG 0.007 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 115 time to evaluate : 0.994 Fit side-chains REVERT: A 185 TYR cc_start: 0.6148 (t80) cc_final: 0.4279 (p90) REVERT: A 304 LEU cc_start: 0.5991 (OUTLIER) cc_final: 0.5715 (pp) REVERT: A 561 ASP cc_start: 0.7682 (p0) cc_final: 0.7356 (p0) REVERT: A 623 LYS cc_start: 0.8251 (ptpt) cc_final: 0.7987 (ptpp) REVERT: B 179 ASP cc_start: 0.6906 (m-30) cc_final: 0.6424 (t0) REVERT: C 76 ARG cc_start: 0.6509 (ttm170) cc_final: 0.5578 (tpt170) REVERT: C 184 MET cc_start: 0.4505 (mtm) cc_final: 0.4249 (mtm) REVERT: C 202 LYS cc_start: 0.6122 (mtpp) cc_final: 0.5522 (mptt) REVERT: C 224 PHE cc_start: 0.3032 (OUTLIER) cc_final: 0.2080 (p90) REVERT: C 253 MET cc_start: 0.5545 (mmm) cc_final: 0.4323 (ptp) outliers start: 37 outliers final: 26 residues processed: 138 average time/residue: 0.1725 time to fit residues: 35.4201 Evaluate side-chains 134 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 155 HIS Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 650 ASP Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 217 HIS Chi-restraints excluded: chain C residue 224 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 193 GLN A 612 HIS B 226 ASN C 122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5709 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9253 Z= 0.243 Angle : 0.593 10.052 12510 Z= 0.303 Chirality : 0.044 0.158 1370 Planarity : 0.004 0.045 1608 Dihedral : 4.790 22.621 1201 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.57 % Allowed : 14.78 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.13 (0.25), residues: 1090 helix: 0.78 (0.30), residues: 294 sheet: -0.76 (0.35), residues: 200 loop : -0.17 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 171 HIS 0.008 0.001 HIS C 328 PHE 0.047 0.002 PHE C 212 TYR 0.014 0.001 TYR C 223 ARG 0.008 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 116 time to evaluate : 1.136 Fit side-chains revert: symmetry clash REVERT: A 185 TYR cc_start: 0.6201 (t80) cc_final: 0.4377 (p90) REVERT: A 304 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5627 (pp) REVERT: A 561 ASP cc_start: 0.7651 (p0) cc_final: 0.7312 (p0) REVERT: A 623 LYS cc_start: 0.8231 (ptpt) cc_final: 0.7965 (ptpp) REVERT: B 179 ASP cc_start: 0.6869 (m-30) cc_final: 0.6385 (t0) REVERT: C 76 ARG cc_start: 0.6469 (ttm170) cc_final: 0.5537 (tpt170) REVERT: C 184 MET cc_start: 0.4477 (mtm) cc_final: 0.4254 (mtm) REVERT: C 202 LYS cc_start: 0.6139 (mtpp) cc_final: 0.5546 (mptt) REVERT: C 224 PHE cc_start: 0.3011 (OUTLIER) cc_final: 0.1891 (p90) REVERT: C 253 MET cc_start: 0.5532 (mmm) cc_final: 0.4323 (ptp) REVERT: C 330 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5746 (tt) outliers start: 36 outliers final: 29 residues processed: 141 average time/residue: 0.1926 time to fit residues: 39.0395 Evaluate side-chains 140 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 108 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 217 HIS Chi-restraints excluded: chain C residue 224 PHE Chi-restraints excluded: chain C residue 330 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.2980 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 0.0270 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 155 HIS A 193 GLN ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5693 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9253 Z= 0.213 Angle : 0.571 8.140 12510 Z= 0.293 Chirality : 0.044 0.158 1370 Planarity : 0.004 0.044 1608 Dihedral : 4.761 24.435 1201 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.47 % Allowed : 15.08 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.13 (0.25), residues: 1090 helix: 0.83 (0.30), residues: 294 sheet: -0.82 (0.34), residues: 213 loop : -0.16 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 171 HIS 0.008 0.001 HIS C 328 PHE 0.041 0.002 PHE C 212 TYR 0.017 0.001 TYR C 223 ARG 0.002 0.000 ARG A 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 111 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 185 TYR cc_start: 0.6190 (t80) cc_final: 0.4443 (p90) REVERT: A 200 TYR cc_start: 0.7254 (m-80) cc_final: 0.6972 (m-80) REVERT: A 304 LEU cc_start: 0.5905 (OUTLIER) cc_final: 0.5688 (pp) REVERT: A 561 ASP cc_start: 0.7664 (p0) cc_final: 0.7332 (p0) REVERT: A 623 LYS cc_start: 0.8219 (ptpt) cc_final: 0.7964 (ptpp) REVERT: B 179 ASP cc_start: 0.6839 (m-30) cc_final: 0.6355 (t0) REVERT: C 76 ARG cc_start: 0.6462 (ttm170) cc_final: 0.5477 (tpt170) REVERT: C 202 LYS cc_start: 0.6171 (mtpp) cc_final: 0.5550 (mmtt) REVERT: C 224 PHE cc_start: 0.3005 (OUTLIER) cc_final: 0.1841 (p90) REVERT: C 253 MET cc_start: 0.5494 (mmm) cc_final: 0.4284 (ptp) REVERT: C 330 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5666 (tt) outliers start: 35 outliers final: 30 residues processed: 135 average time/residue: 0.1907 time to fit residues: 37.8247 Evaluate side-chains 141 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 108 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 193 GLN Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 982 MET Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 217 HIS Chi-restraints excluded: chain C residue 224 PHE Chi-restraints excluded: chain C residue 330 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 8.9990 chunk 73 optimal weight: 0.5980 chunk 110 optimal weight: 0.0980 chunk 101 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.0670 chunk 26 optimal weight: 0.9980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 577 HIS B 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5668 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9253 Z= 0.183 Angle : 0.557 8.321 12510 Z= 0.285 Chirality : 0.044 0.158 1370 Planarity : 0.004 0.045 1608 Dihedral : 4.686 25.443 1201 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.27 % Allowed : 15.38 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.01 (0.25), residues: 1090 helix: 0.90 (0.30), residues: 295 sheet: -0.66 (0.35), residues: 200 loop : -0.13 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 171 HIS 0.008 0.001 HIS C 328 PHE 0.043 0.002 PHE C 212 TYR 0.017 0.001 TYR C 223 ARG 0.002 0.000 ARG A 569 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 113 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 185 TYR cc_start: 0.6123 (t80) cc_final: 0.4447 (p90) REVERT: A 200 TYR cc_start: 0.7235 (m-80) cc_final: 0.6963 (m-80) REVERT: A 561 ASP cc_start: 0.7633 (p0) cc_final: 0.7303 (p0) REVERT: A 623 LYS cc_start: 0.8208 (ptpt) cc_final: 0.8008 (ptpp) REVERT: B 179 ASP cc_start: 0.6857 (m-30) cc_final: 0.6344 (t0) REVERT: B 191 PRO cc_start: 0.6937 (Cg_exo) cc_final: 0.6714 (Cg_endo) REVERT: C 76 ARG cc_start: 0.6440 (ttm170) cc_final: 0.5465 (tpt170) REVERT: C 202 LYS cc_start: 0.6148 (mtpp) cc_final: 0.5542 (mmtt) REVERT: C 224 PHE cc_start: 0.3061 (OUTLIER) cc_final: 0.1889 (p90) REVERT: C 253 MET cc_start: 0.5513 (mmm) cc_final: 0.4240 (ptp) REVERT: C 330 LEU cc_start: 0.5889 (OUTLIER) cc_final: 0.5553 (tt) outliers start: 33 outliers final: 28 residues processed: 135 average time/residue: 0.1794 time to fit residues: 35.7518 Evaluate side-chains 139 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 577 HIS Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 217 HIS Chi-restraints excluded: chain C residue 224 PHE Chi-restraints excluded: chain C residue 330 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 30.0000 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 77 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 63 optimal weight: 10.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 577 HIS B 226 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.276708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.226441 restraints weight = 8603.517| |-----------------------------------------------------------------------------| r_work (start): 0.4608 rms_B_bonded: 3.58 r_work: 0.4224 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9253 Z= 0.190 Angle : 0.558 8.275 12510 Z= 0.285 Chirality : 0.044 0.159 1370 Planarity : 0.004 0.053 1608 Dihedral : 4.676 25.723 1201 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.17 % Allowed : 15.77 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.01 (0.26), residues: 1090 helix: 0.92 (0.30), residues: 295 sheet: -0.70 (0.35), residues: 211 loop : -0.08 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 171 HIS 0.008 0.001 HIS C 328 PHE 0.043 0.002 PHE C 212 TYR 0.016 0.001 TYR C 223 ARG 0.006 0.000 ARG B 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2153.09 seconds wall clock time: 41 minutes 4.51 seconds (2464.51 seconds total)