Starting phenix.real_space_refine on Wed Feb 14 14:06:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un3_26612/02_2024/7un3_26612.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un3_26612/02_2024/7un3_26612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un3_26612/02_2024/7un3_26612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un3_26612/02_2024/7un3_26612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un3_26612/02_2024/7un3_26612.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un3_26612/02_2024/7un3_26612.pdb" } resolution = 3.5 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= 0.043 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 6056 2.51 5 N 1605 2.21 5 O 1721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A ASP 556": "OD1" <-> "OD2" Residue "A PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 632": "OE1" <-> "OE2" Residue "A GLU 637": "OE1" <-> "OE2" Residue "A GLU 691": "OE1" <-> "OE2" Residue "A GLU 961": "OE1" <-> "OE2" Residue "A GLU 1124": "OE1" <-> "OE2" Residue "A GLU 1126": "OE1" <-> "OE2" Residue "A PHE 1256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 301": "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: 9423 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "A" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5196 Classifications: {'peptide': 649} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 611} Chain breaks: 9 Chain: "B" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1838 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain breaks: 2 Chain: "C" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1807 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain breaks: 2 Time building chain proxies: 5.43, per 1000 atoms: 0.58 Number of scatterers: 9423 At special positions: 0 Unit cell: (83.325, 113.025, 141.075, 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 1721 8.00 N 1605 7.00 C 6056 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: 3.49 Conformation dependent library (CDL) restraints added in 2.0 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 32.2% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'D' and resid 22 through 35 removed outlier: 3.589A pdb=" N VAL D 26 " --> pdb=" O THR D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'A' and resid 127 through 130 removed outlier: 4.145A pdb=" N GLY A 130 " --> pdb=" O TYR A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 127 through 130' Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.523A pdb=" N LYS A 139 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 271 through 275 removed outlier: 4.429A pdb=" N SER A 275 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 336 removed outlier: 4.399A pdb=" N GLY A 334 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 335 " --> pdb=" O ASN A 332 " (cutoff:3.500A) 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 removed outlier: 3.559A pdb=" N LYS A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1045 Processing helix chain 'A' and resid 1060 through 1071 Processing helix chain 'A' and resid 1076 through 1080 removed outlier: 3.531A pdb=" N ASN A1080 " --> pdb=" O PRO A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1088 removed outlier: 3.806A pdb=" N ARG A1088 " --> pdb=" O ASP A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1118 Processing helix chain 'A' and resid 1123 through 1133 Processing helix chain 'A' and resid 1134 through 1152 removed outlier: 4.049A pdb=" N VAL A1139 " --> pdb=" O GLY A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1283 removed outlier: 3.708A pdb=" N GLN A1275 " --> pdb=" O GLY A1271 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 121 removed outlier: 3.860A pdb=" N VAL B 108 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 169 through 177 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 188 through 194 removed outlier: 4.194A pdb=" N ILE B 192 " --> pdb=" O HIS B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 302 Processing helix chain 'B' and resid 320 through 333 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.776A pdb=" N TYR B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 122 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 removed outlier: 3.826A pdb=" N ASP C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'C' and resid 296 through 302 removed outlier: 4.150A pdb=" N PHE C 300 " --> pdb=" O PHE C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 333 Processing sheet with id=AA1, first strand: chain 'D' and resid 12 through 16 removed outlier: 4.102A pdb=" N SER D 65 " --> pdb=" O GLN D 2 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 132 through 134 removed outlier: 6.787A pdb=" N ARG A 123 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N SER A 67 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU A 142 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 188 removed outlier: 6.624A pdb=" N ILE A 183 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU A 177 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N TYR A 185 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL A 175 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N VAL A 166 " --> pdb=" O MET A 558 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N MET A 558 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP A 168 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL A 557 " --> pdb=" O CYS A 566 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N CYS A 566 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TRP A 559 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL A 564 " --> pdb=" O TRP A 559 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 194 removed outlier: 6.187A pdb=" N ALA A 174 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 269 removed outlier: 6.187A pdb=" N VAL A 295 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU A 224 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLU A 297 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU A 222 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 299 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE A 220 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL A 301 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASN A 218 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU A 303 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU A 216 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS A 305 " --> pdb=" O TYR A 214 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU A 210 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 277 through 280 removed outlier: 5.524A pdb=" N TRP A 278 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER A 231 " --> pdb=" O TRP A 278 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU A 210 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS A 305 " --> pdb=" O TYR A 214 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU A 216 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU A 303 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASN A 218 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL A 301 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE A 220 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 299 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU A 222 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLU A 297 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU A 224 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL A 295 " --> pdb=" O LEU A 224 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 291 through 311 current: chain 'A' and resid 337 through 338 Processing sheet with id=AA7, first strand: chain 'A' and resid 631 through 641 removed outlier: 5.333A pdb=" N LEU A 633 " --> pdb=" O LYS A 623 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS A 623 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP A 639 " --> pdb=" O CYS A 617 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N CYS A 617 " --> pdb=" O ASP A 639 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A 609 " --> pdb=" O MET A 618 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS A 620 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL A 607 " --> pdb=" O LYS A 620 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE A 622 " --> pdb=" O GLY A 605 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLY A 605 " --> pdb=" O PHE A 622 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 698 through 702 removed outlier: 3.985A pdb=" N SER A 698 " --> pdb=" O TRP A 694 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU A 691 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 931 through 932 removed outlier: 3.541A pdb=" N PHE A 978 " --> pdb=" O LEU A 984 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU A 984 " --> pdb=" O PHE A 978 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 196 through 203 removed outlier: 3.635A pdb=" N PHE B 212 " --> pdb=" O TYR B 233 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 214 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS B 231 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY B 254 " --> pdb=" O ARG B 234 " (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 196 through 203 removed outlier: 3.716A pdb=" N THR C 232 " --> pdb=" O THR C 256 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ARG C 234 " --> pdb=" O GLY C 254 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLY C 254 " --> pdb=" O ARG C 234 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 270 through 278 379 hydrogen bonds defined for protein. 1053 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: 3.15 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3043 1.34 - 1.46: 1868 1.46 - 1.58: 4661 1.58 - 1.70: 0 1.70 - 1.81: 62 Bond restraints: 9634 Sorted by residual: bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" CG LEU C 81 " pdb=" CD2 LEU C 81 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.50e+00 bond pdb=" CB TRP A 308 " pdb=" CG TRP A 308 " ideal model delta sigma weight residual 1.498 1.469 0.029 3.10e-02 1.04e+03 9.02e-01 bond pdb=" CG LYS C 231 " pdb=" CD LYS C 231 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.95e-01 bond pdb=" CE LYS C 231 " pdb=" NZ LYS C 231 " ideal model delta sigma weight residual 1.489 1.461 0.028 3.00e-02 1.11e+03 8.66e-01 ... (remaining 9629 not shown) Histogram of bond angle deviations from ideal: 98.93 - 105.94: 243 105.94 - 112.96: 5196 112.96 - 119.97: 3235 119.97 - 126.98: 4225 126.98 - 133.99: 117 Bond angle restraints: 13016 Sorted by residual: angle pdb=" CA ARG A1128 " pdb=" CB ARG A1128 " pdb=" CG ARG A1128 " ideal model delta sigma weight residual 114.10 121.80 -7.70 2.00e+00 2.50e-01 1.48e+01 angle pdb=" CA GLN B 111 " pdb=" C GLN B 111 " pdb=" N PRO B 112 " ideal model delta sigma weight residual 118.44 122.78 -4.34 1.59e+00 3.96e-01 7.44e+00 angle pdb=" CA MET A1285 " pdb=" CB MET A1285 " pdb=" CG MET A1285 " ideal model delta sigma weight residual 114.10 119.35 -5.25 2.00e+00 2.50e-01 6.90e+00 angle pdb=" CB LYS A 136 " pdb=" CG LYS A 136 " pdb=" CD LYS A 136 " ideal model delta sigma weight residual 111.30 117.14 -5.84 2.30e+00 1.89e-01 6.45e+00 angle pdb=" N ASN A1080 " pdb=" CA ASN A1080 " pdb=" C ASN A1080 " ideal model delta sigma weight residual 111.56 115.06 -3.50 1.38e+00 5.25e-01 6.44e+00 ... (remaining 13011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5274 17.83 - 35.65: 446 35.65 - 53.48: 75 53.48 - 71.31: 12 71.31 - 89.13: 8 Dihedral angle restraints: 5815 sinusoidal: 2431 harmonic: 3384 Sorted by residual: dihedral pdb=" CA ARG B 333 " pdb=" C ARG B 333 " pdb=" N ILE B 334 " pdb=" CA ILE B 334 " ideal model delta harmonic sigma weight residual 180.00 -162.44 -17.56 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA PHE B 224 " pdb=" C PHE B 224 " pdb=" N THR B 225 " pdb=" CA THR B 225 " ideal model delta harmonic sigma weight residual -180.00 -162.71 -17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASN A 582 " pdb=" C ASN A 582 " pdb=" N GLU A 583 " pdb=" CA GLU A 583 " ideal model delta harmonic sigma weight residual 180.00 163.36 16.64 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 5812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1036 0.039 - 0.078: 252 0.078 - 0.117: 122 0.117 - 0.156: 29 0.156 - 0.195: 2 Chirality restraints: 1441 Sorted by residual: chirality pdb=" CB ILE A1127 " pdb=" CA ILE A1127 " pdb=" CG1 ILE A1127 " pdb=" CG2 ILE A1127 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.46e-01 chirality pdb=" CA GLN B 111 " pdb=" N GLN B 111 " pdb=" C GLN B 111 " pdb=" CB GLN B 111 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA ILE A1254 " pdb=" N ILE A1254 " pdb=" C ILE A1254 " pdb=" CB ILE A1254 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 1438 not shown) Planarity restraints: 1665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A1256 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO A1257 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A1257 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A1257 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 303 " 0.046 5.00e-02 4.00e+02 6.94e-02 7.71e+00 pdb=" N PRO C 304 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 304 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 304 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A1012 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO A1013 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A1013 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A1013 " 0.025 5.00e-02 4.00e+02 ... (remaining 1662 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 104 2.53 - 3.12: 7859 3.12 - 3.71: 14619 3.71 - 4.31: 20351 4.31 - 4.90: 33811 Nonbonded interactions: 76744 Sorted by model distance: nonbonded pdb=" OD1 ASP A 144 " pdb=" OG1 THR A 553 " model vdw 1.936 2.440 nonbonded pdb=" NH1 ARG A 154 " pdb=" O SER A 161 " model vdw 1.968 2.520 nonbonded pdb=" OG SER A1023 " pdb=" O ASP A1035 " model vdw 2.003 2.440 nonbonded pdb=" N SER C 296 " pdb=" OD1 ASN C 299 " model vdw 2.092 2.520 nonbonded pdb=" NH1 ARG D 54 " pdb=" OD2 ASP D 58 " model vdw 2.119 2.520 ... (remaining 76739 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 121 or resid 166 through 342)) selection = (chain 'C' and (resid 73 through 121 or resid 166 through 306 or resid 319 throu \ gh 342)) } 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 group one per residue 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: 1.600 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: 0.140 Set scattering table: 0.090 Process input model: 28.490 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6182 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 : 0.003 0.040 9634 Z= 0.197 Angle : 0.612 7.699 13016 Z= 0.335 Chirality : 0.044 0.195 1441 Planarity : 0.005 0.071 1665 Dihedral : 13.626 89.132 3613 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1130 helix: 0.62 (0.30), residues: 303 sheet: -0.75 (0.32), residues: 254 loop : -1.12 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 171 HIS 0.006 0.001 HIS B 328 PHE 0.014 0.001 PHE A 622 TYR 0.021 0.002 TYR A1100 ARG 0.015 0.001 ARG A1088 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 GLN cc_start: 0.5815 (tm-30) cc_final: 0.5500 (tm-30) REVERT: A 58 ARG cc_start: 0.7121 (ptm160) cc_final: 0.6799 (ptm160) REVERT: A 156 MET cc_start: 0.7240 (mtp) cc_final: 0.6997 (mtt) REVERT: A 171 ILE cc_start: 0.7482 (mm) cc_final: 0.6787 (mm) REVERT: A 190 LYS cc_start: 0.7344 (mmtt) cc_final: 0.7097 (tppt) REVERT: A 577 HIS cc_start: 0.6000 (m-70) cc_final: 0.5772 (m-70) REVERT: A 1084 PHE cc_start: 0.6401 (m-80) cc_final: 0.5451 (m-80) REVERT: B 205 ASP cc_start: 0.7709 (m-30) cc_final: 0.7392 (m-30) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.2265 time to fit residues: 78.0481 Evaluate side-chains 179 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 0.0970 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 overall best weight: 1.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 170 ASN ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN A 582 ASN B 188 HIS ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6381 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9634 Z= 0.308 Angle : 0.682 7.653 13016 Z= 0.354 Chirality : 0.048 0.194 1441 Planarity : 0.005 0.048 1665 Dihedral : 5.133 22.414 1246 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.80 % Allowed : 11.17 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: 1130 helix: 0.85 (0.30), residues: 294 sheet: -0.57 (0.33), residues: 248 loop : -1.00 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1145 HIS 0.009 0.001 HIS B 328 PHE 0.026 0.002 PHE A1084 TYR 0.019 0.002 TYR C 233 ARG 0.017 0.001 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 197 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 GLN cc_start: 0.6080 (tm-30) cc_final: 0.5871 (tm-30) REVERT: A 156 MET cc_start: 0.7419 (mtp) cc_final: 0.7217 (mtt) REVERT: A 190 LYS cc_start: 0.7228 (mmtt) cc_final: 0.7002 (tppt) REVERT: A 199 MET cc_start: 0.7183 (mtp) cc_final: 0.6800 (mtp) REVERT: A 552 MET cc_start: 0.6525 (ttt) cc_final: 0.6317 (ttp) REVERT: A 1084 PHE cc_start: 0.6716 (m-80) cc_final: 0.6433 (m-80) REVERT: A 1285 MET cc_start: 0.5980 (mmp) cc_final: 0.5727 (mmt) REVERT: B 110 TYR cc_start: 0.7172 (OUTLIER) cc_final: 0.6947 (t80) REVERT: B 179 ASP cc_start: 0.6612 (m-30) cc_final: 0.6395 (p0) REVERT: C 210 MET cc_start: 0.7238 (mtm) cc_final: 0.6934 (mtm) outliers start: 19 outliers final: 12 residues processed: 204 average time/residue: 0.2236 time to fit residues: 62.6173 Evaluate side-chains 172 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain C residue 330 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 86 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 170 ASN ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9634 Z= 0.252 Angle : 0.629 8.056 13016 Z= 0.324 Chirality : 0.046 0.187 1441 Planarity : 0.005 0.050 1665 Dihedral : 4.988 19.123 1246 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.94 % Allowed : 12.59 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -0.64 (0.25), residues: 1130 helix: 0.77 (0.30), residues: 303 sheet: -0.65 (0.33), residues: 248 loop : -0.92 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 308 HIS 0.007 0.001 HIS B 328 PHE 0.014 0.002 PHE B 218 TYR 0.014 0.002 TYR C 106 ARG 0.003 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 178 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6593 (ptm) REVERT: D 31 GLN cc_start: 0.6100 (tm-30) cc_final: 0.5897 (tm-30) REVERT: A 156 MET cc_start: 0.7500 (mtp) cc_final: 0.7295 (mtt) REVERT: A 271 LYS cc_start: 0.7555 (mmmt) cc_final: 0.7181 (mmtm) REVERT: A 552 MET cc_start: 0.6503 (ttt) cc_final: 0.6237 (ttp) REVERT: B 110 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.6712 (t80) REVERT: B 118 PHE cc_start: 0.7323 (t80) cc_final: 0.6963 (t80) REVERT: B 210 MET cc_start: 0.5398 (mpp) cc_final: 0.5142 (mpp) REVERT: B 221 ASN cc_start: 0.7840 (p0) cc_final: 0.7563 (p0) REVERT: C 170 PHE cc_start: 0.3923 (t80) cc_final: 0.3656 (t80) REVERT: C 171 TRP cc_start: 0.6413 (m-90) cc_final: 0.4790 (m-90) REVERT: C 210 MET cc_start: 0.7547 (mtm) cc_final: 0.7282 (mtm) outliers start: 31 outliers final: 17 residues processed: 194 average time/residue: 0.2309 time to fit residues: 62.7457 Evaluate side-chains 182 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 163 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 330 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 0.0870 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 110 optimal weight: 20.0000 chunk 54 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN A 581 ASN ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9634 Z= 0.359 Angle : 0.674 7.246 13016 Z= 0.350 Chirality : 0.047 0.176 1441 Planarity : 0.005 0.047 1665 Dihedral : 5.211 21.307 1246 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.41 % Allowed : 15.44 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.25), residues: 1130 helix: 0.90 (0.30), residues: 290 sheet: -0.59 (0.34), residues: 235 loop : -1.11 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 278 HIS 0.005 0.001 HIS A 155 PHE 0.021 0.002 PHE A1084 TYR 0.013 0.002 TYR A 355 ARG 0.014 0.001 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 173 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6631 (ptm) REVERT: D 31 GLN cc_start: 0.6096 (tm-30) cc_final: 0.5773 (tm-30) REVERT: A 133 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7585 (pt0) REVERT: A 156 MET cc_start: 0.7505 (mtp) cc_final: 0.7268 (mtt) REVERT: A 271 LYS cc_start: 0.7358 (mmmt) cc_final: 0.6967 (mmtm) REVERT: A 552 MET cc_start: 0.6481 (ttt) cc_final: 0.6242 (ttp) REVERT: B 110 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.7079 (t80) REVERT: B 118 PHE cc_start: 0.7539 (t80) cc_final: 0.7072 (t80) REVERT: B 179 ASP cc_start: 0.7399 (m-30) cc_final: 0.6966 (p0) REVERT: B 221 ASN cc_start: 0.7898 (p0) cc_final: 0.7559 (p0) REVERT: B 236 ARG cc_start: 0.7177 (mtp180) cc_final: 0.6918 (mtp180) REVERT: B 261 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7451 (p0) REVERT: C 97 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8220 (mm-30) REVERT: C 170 PHE cc_start: 0.4011 (t80) cc_final: 0.3455 (t80) REVERT: C 171 TRP cc_start: 0.6658 (m-90) cc_final: 0.6095 (m-90) outliers start: 36 outliers final: 21 residues processed: 195 average time/residue: 0.1910 time to fit residues: 53.6362 Evaluate side-chains 180 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 330 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.0980 chunk 62 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 27 optimal weight: 0.0060 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 170 ASN ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN A 582 ASN A1275 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9634 Z= 0.181 Angle : 0.596 12.064 13016 Z= 0.306 Chirality : 0.045 0.233 1441 Planarity : 0.005 0.041 1665 Dihedral : 4.856 18.953 1246 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.31 % Allowed : 17.42 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -0.40 (0.25), residues: 1130 helix: 1.33 (0.31), residues: 283 sheet: -0.68 (0.34), residues: 241 loop : -0.83 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1145 HIS 0.003 0.001 HIS A 155 PHE 0.012 0.002 PHE B 218 TYR 0.012 0.001 TYR B 96 ARG 0.004 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 179 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6568 (ptm) REVERT: D 31 GLN cc_start: 0.6113 (tm-30) cc_final: 0.5709 (tm-30) REVERT: A 156 MET cc_start: 0.7469 (mtp) cc_final: 0.7218 (mtt) REVERT: A 271 LYS cc_start: 0.7419 (mmmt) cc_final: 0.7015 (mmtm) REVERT: A 1114 GLN cc_start: 0.7278 (tm-30) cc_final: 0.6869 (tm-30) REVERT: B 85 GLN cc_start: 0.8136 (tp-100) cc_final: 0.7646 (mm-40) REVERT: B 110 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.6937 (t80) REVERT: B 118 PHE cc_start: 0.7370 (t80) cc_final: 0.7054 (t80) REVERT: B 179 ASP cc_start: 0.6980 (m-30) cc_final: 0.6584 (p0) REVERT: B 221 ASN cc_start: 0.7763 (p0) cc_final: 0.7489 (p0) REVERT: B 236 ARG cc_start: 0.7221 (mtp180) cc_final: 0.7000 (mtp180) REVERT: C 97 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8186 (mm-30) REVERT: C 170 PHE cc_start: 0.3892 (t80) cc_final: 0.3446 (t80) REVERT: C 171 TRP cc_start: 0.6489 (m-90) cc_final: 0.5748 (m-90) outliers start: 35 outliers final: 21 residues processed: 198 average time/residue: 0.2004 time to fit residues: 56.2042 Evaluate side-chains 192 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 169 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 581 ASN Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 330 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 0.0050 chunk 110 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 0.0030 overall best weight: 0.9408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 170 ASN ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9634 Z= 0.231 Angle : 0.607 10.467 13016 Z= 0.314 Chirality : 0.045 0.208 1441 Planarity : 0.005 0.043 1665 Dihedral : 4.819 19.209 1246 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.12 % Allowed : 18.37 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -0.42 (0.25), residues: 1130 helix: 1.33 (0.31), residues: 288 sheet: -0.77 (0.34), residues: 244 loop : -0.84 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1145 HIS 0.004 0.001 HIS A 155 PHE 0.018 0.002 PHE A 292 TYR 0.009 0.001 TYR B 96 ARG 0.004 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 168 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6526 (ptm) REVERT: D 31 GLN cc_start: 0.6182 (tm-30) cc_final: 0.5779 (tm-30) REVERT: D 54 ARG cc_start: 0.6568 (OUTLIER) cc_final: 0.6079 (ttt180) REVERT: A 156 MET cc_start: 0.7491 (mtp) cc_final: 0.7254 (mtt) REVERT: A 271 LYS cc_start: 0.7414 (mmmt) cc_final: 0.7032 (mmtm) REVERT: A 974 MET cc_start: 0.7361 (pmm) cc_final: 0.7109 (pmm) REVERT: A 982 MET cc_start: 0.5904 (mmm) cc_final: 0.4966 (tpt) REVERT: A 1013 PRO cc_start: 0.7646 (Cg_endo) cc_final: 0.7047 (Cg_exo) REVERT: A 1114 GLN cc_start: 0.7230 (tm-30) cc_final: 0.6830 (tm-30) REVERT: B 85 GLN cc_start: 0.8143 (tp-100) cc_final: 0.7671 (mm-40) REVERT: B 118 PHE cc_start: 0.7332 (t80) cc_final: 0.6946 (t80) REVERT: B 221 ASN cc_start: 0.7799 (p0) cc_final: 0.7537 (p0) REVERT: B 345 GLU cc_start: 0.7862 (tp30) cc_final: 0.7547 (tp30) REVERT: C 83 ASN cc_start: 0.8338 (m-40) cc_final: 0.8013 (m110) REVERT: C 170 PHE cc_start: 0.3854 (t80) cc_final: 0.3387 (t80) REVERT: C 171 TRP cc_start: 0.6537 (m-90) cc_final: 0.5679 (m-90) outliers start: 33 outliers final: 26 residues processed: 184 average time/residue: 0.1965 time to fit residues: 51.6436 Evaluate side-chains 182 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 330 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 80 optimal weight: 0.2980 chunk 92 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9634 Z= 0.211 Angle : 0.607 9.729 13016 Z= 0.312 Chirality : 0.045 0.209 1441 Planarity : 0.004 0.046 1665 Dihedral : 4.768 20.183 1246 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.12 % Allowed : 18.56 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.25), residues: 1130 helix: 1.27 (0.31), residues: 294 sheet: -0.78 (0.34), residues: 230 loop : -0.87 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1145 HIS 0.004 0.001 HIS A 578 PHE 0.015 0.002 PHE A 292 TYR 0.012 0.001 TYR C 106 ARG 0.003 0.000 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.6450 (ptm) REVERT: D 31 GLN cc_start: 0.6124 (tm-30) cc_final: 0.5724 (tm-30) REVERT: D 54 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.6092 (ttt180) REVERT: A 156 MET cc_start: 0.7465 (mtp) cc_final: 0.7225 (mtt) REVERT: A 199 MET cc_start: 0.7060 (mtp) cc_final: 0.6667 (mtt) REVERT: A 260 PHE cc_start: 0.6720 (m-10) cc_final: 0.6457 (m-10) REVERT: A 271 LYS cc_start: 0.7412 (mmmt) cc_final: 0.7030 (mmtm) REVERT: A 1013 PRO cc_start: 0.7750 (Cg_endo) cc_final: 0.7141 (Cg_exo) REVERT: B 85 GLN cc_start: 0.8129 (tp-100) cc_final: 0.7659 (mm-40) REVERT: B 110 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.6936 (t80) REVERT: B 118 PHE cc_start: 0.7244 (t80) cc_final: 0.6938 (t80) REVERT: B 221 ASN cc_start: 0.7794 (p0) cc_final: 0.7544 (p0) REVERT: B 236 ARG cc_start: 0.7257 (mtp180) cc_final: 0.6929 (mtp180) REVERT: B 345 GLU cc_start: 0.7881 (tp30) cc_final: 0.7581 (tp30) REVERT: C 83 ASN cc_start: 0.8352 (m-40) cc_final: 0.8058 (m110) REVERT: C 170 PHE cc_start: 0.3802 (t80) cc_final: 0.3393 (t80) REVERT: C 171 TRP cc_start: 0.6538 (m-90) cc_final: 0.5933 (m-90) outliers start: 33 outliers final: 26 residues processed: 182 average time/residue: 0.2033 time to fit residues: 52.4664 Evaluate side-chains 187 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 581 ASN Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 330 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 86 optimal weight: 0.0000 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 0.0000 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1024 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9634 Z= 0.265 Angle : 0.639 9.200 13016 Z= 0.329 Chirality : 0.046 0.232 1441 Planarity : 0.005 0.043 1665 Dihedral : 4.852 20.033 1246 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.69 % Allowed : 19.03 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -0.58 (0.25), residues: 1130 helix: 1.19 (0.31), residues: 295 sheet: -0.91 (0.34), residues: 229 loop : -0.94 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1145 HIS 0.005 0.001 HIS A 578 PHE 0.016 0.002 PHE A 574 TYR 0.010 0.001 TYR C 96 ARG 0.003 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 160 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6365 (ptm) REVERT: D 31 GLN cc_start: 0.5986 (tm-30) cc_final: 0.5652 (tm-30) REVERT: D 54 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.5981 (ttt-90) REVERT: A 156 MET cc_start: 0.7420 (mtp) cc_final: 0.7168 (mtt) REVERT: A 171 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7220 (mm) REVERT: A 271 LYS cc_start: 0.7385 (mmmt) cc_final: 0.6983 (mmtm) REVERT: A 982 MET cc_start: 0.5697 (mmm) cc_final: 0.5129 (tpt) REVERT: A 1013 PRO cc_start: 0.7876 (Cg_endo) cc_final: 0.7271 (Cg_exo) REVERT: B 85 GLN cc_start: 0.8147 (tp-100) cc_final: 0.7661 (mm-40) REVERT: B 110 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6864 (t80) REVERT: B 118 PHE cc_start: 0.7222 (t80) cc_final: 0.6861 (t80) REVERT: B 179 ASP cc_start: 0.7263 (m-30) cc_final: 0.6848 (p0) REVERT: B 221 ASN cc_start: 0.7886 (p0) cc_final: 0.7587 (p0) REVERT: B 236 ARG cc_start: 0.7227 (mtp180) cc_final: 0.6997 (mtp180) REVERT: B 345 GLU cc_start: 0.7810 (tp30) cc_final: 0.7529 (tp30) REVERT: C 83 ASN cc_start: 0.8445 (m-40) cc_final: 0.8102 (m110) REVERT: C 170 PHE cc_start: 0.3820 (t80) cc_final: 0.3244 (t80) REVERT: C 171 TRP cc_start: 0.6679 (m-90) cc_final: 0.6407 (m-90) REVERT: C 180 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.6154 (mm) REVERT: C 210 MET cc_start: 0.7832 (mtm) cc_final: 0.7577 (mtm) outliers start: 39 outliers final: 24 residues processed: 182 average time/residue: 0.2129 time to fit residues: 55.2567 Evaluate side-chains 183 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 330 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 0.0870 chunk 61 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 108 optimal weight: 0.0970 chunk 66 optimal weight: 0.9980 overall best weight: 0.6156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1024 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9634 Z= 0.197 Angle : 0.613 8.637 13016 Z= 0.313 Chirality : 0.045 0.187 1441 Planarity : 0.004 0.040 1665 Dihedral : 4.715 20.924 1246 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.31 % Allowed : 19.13 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -0.48 (0.25), residues: 1130 helix: 1.19 (0.31), residues: 294 sheet: -0.88 (0.34), residues: 225 loop : -0.82 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1145 HIS 0.006 0.001 HIS A 578 PHE 0.015 0.002 PHE A 292 TYR 0.010 0.001 TYR C 106 ARG 0.003 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 165 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6332 (ptm) REVERT: D 31 GLN cc_start: 0.6005 (tm-30) cc_final: 0.5696 (tm-30) REVERT: D 54 ARG cc_start: 0.6547 (OUTLIER) cc_final: 0.6035 (ttt-90) REVERT: A 156 MET cc_start: 0.7370 (mtp) cc_final: 0.7125 (mtt) REVERT: A 171 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7241 (mm) REVERT: A 185 TYR cc_start: 0.6810 (t80) cc_final: 0.6378 (t80) REVERT: A 199 MET cc_start: 0.7071 (mtp) cc_final: 0.6740 (mtt) REVERT: A 271 LYS cc_start: 0.7377 (mmmt) cc_final: 0.7014 (mmtm) REVERT: A 982 MET cc_start: 0.5818 (mmm) cc_final: 0.5161 (tpt) REVERT: A 1013 PRO cc_start: 0.7871 (Cg_endo) cc_final: 0.7264 (Cg_exo) REVERT: B 85 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7628 (mm-40) REVERT: B 118 PHE cc_start: 0.7179 (t80) cc_final: 0.6889 (t80) REVERT: B 221 ASN cc_start: 0.7799 (p0) cc_final: 0.7561 (p0) REVERT: B 345 GLU cc_start: 0.7698 (tp30) cc_final: 0.7458 (tp30) REVERT: C 83 ASN cc_start: 0.8433 (m-40) cc_final: 0.8102 (m110) REVERT: C 106 TYR cc_start: 0.8573 (m-80) cc_final: 0.8340 (m-80) REVERT: C 170 PHE cc_start: 0.3976 (t80) cc_final: 0.3393 (t80) REVERT: C 180 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.6223 (mm) REVERT: C 210 MET cc_start: 0.7735 (mtm) cc_final: 0.7532 (mtm) outliers start: 35 outliers final: 25 residues processed: 185 average time/residue: 0.1947 time to fit residues: 51.6060 Evaluate side-chains 188 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 581 ASN Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 330 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 0.0170 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9634 Z= 0.244 Angle : 0.647 8.647 13016 Z= 0.332 Chirality : 0.046 0.187 1441 Planarity : 0.005 0.042 1665 Dihedral : 4.804 22.341 1246 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.94 % Allowed : 19.98 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -0.43 (0.25), residues: 1130 helix: 1.35 (0.31), residues: 288 sheet: -0.87 (0.34), residues: 228 loop : -0.82 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 171 HIS 0.005 0.001 HIS A 578 PHE 0.016 0.002 PHE B 118 TYR 0.010 0.001 TYR C 106 ARG 0.004 0.000 ARG A1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6388 (ptm) REVERT: D 31 GLN cc_start: 0.6015 (tm-30) cc_final: 0.5718 (tm-30) REVERT: D 54 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.5986 (ttt180) REVERT: A 156 MET cc_start: 0.7352 (mtp) cc_final: 0.7107 (mtt) REVERT: A 171 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7315 (mm) REVERT: A 199 MET cc_start: 0.7074 (mtp) cc_final: 0.6735 (mtt) REVERT: A 271 LYS cc_start: 0.7354 (mmmt) cc_final: 0.6961 (mmtm) REVERT: A 552 MET cc_start: 0.6559 (OUTLIER) cc_final: 0.6332 (ppp) REVERT: A 982 MET cc_start: 0.5959 (mmm) cc_final: 0.5341 (tpt) REVERT: A 1013 PRO cc_start: 0.8014 (Cg_endo) cc_final: 0.7434 (Cg_exo) REVERT: B 85 GLN cc_start: 0.8132 (tp-100) cc_final: 0.7672 (mm-40) REVERT: B 118 PHE cc_start: 0.7220 (t80) cc_final: 0.6828 (t80) REVERT: B 221 ASN cc_start: 0.7878 (p0) cc_final: 0.7612 (p0) REVERT: B 236 ARG cc_start: 0.7116 (mtp180) cc_final: 0.6497 (ttt180) REVERT: B 345 GLU cc_start: 0.7700 (tp30) cc_final: 0.7449 (tp30) REVERT: C 83 ASN cc_start: 0.8458 (m-40) cc_final: 0.8118 (m110) REVERT: C 106 TYR cc_start: 0.8566 (m-80) cc_final: 0.8327 (m-80) REVERT: C 170 PHE cc_start: 0.3564 (t80) cc_final: 0.3151 (t80) REVERT: C 180 LEU cc_start: 0.6389 (OUTLIER) cc_final: 0.6167 (mm) outliers start: 31 outliers final: 24 residues processed: 176 average time/residue: 0.1941 time to fit residues: 49.0556 Evaluate side-chains 185 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 156 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 692 VAL Chi-restraints excluded: chain B residue 88 CYS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 330 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.204131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.163316 restraints weight = 15042.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.168051 restraints weight = 8886.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.168682 restraints weight = 6164.312| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9634 Z= 0.231 Angle : 0.641 8.377 13016 Z= 0.330 Chirality : 0.046 0.186 1441 Planarity : 0.005 0.042 1665 Dihedral : 4.794 21.584 1246 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.94 % Allowed : 20.36 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % 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: -0.39 (0.25), residues: 1130 helix: 1.38 (0.31), residues: 283 sheet: -0.79 (0.34), residues: 221 loop : -0.81 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.004 TRP C 171 HIS 0.004 0.001 HIS A 155 PHE 0.021 0.002 PHE C 114 TYR 0.009 0.001 TYR C 110 ARG 0.004 0.000 ARG A1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2252.31 seconds wall clock time: 41 minutes 36.48 seconds (2496.48 seconds total)