Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 09:35:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un3_26612/04_2023/7un3_26612.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un3_26612/04_2023/7un3_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_26612/04_2023/7un3_26612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un3_26612/04_2023/7un3_26612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un3_26612/04_2023/7un3_26612.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un3_26612/04_2023/7un3_26612.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 5.37, per 1000 atoms: 0.57 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: 3.59 Conformation dependent library (CDL) restraints added in 1.4 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: 0.61 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: 3.47 Time building geometry restraints manager: 3.90 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: 1.670 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: 8.820 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.220 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.140 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.096 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 outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.2270 time to fit residues: 78.2771 Evaluate side-chains 177 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6229 ------------------------------------------------------------------------------- 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: 0.2980 chunk 54 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 overall best weight: 1.1580 ------------------------------------------------------------------------------- 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 578 HIS ** 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: 0.6364 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 9634 Z= 0.287 Angle : 0.675 7.722 13016 Z= 0.351 Chirality : 0.048 0.198 1441 Planarity : 0.005 0.047 1665 Dihedral : 5.132 22.222 1246 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 1.89 % 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: 0.86 (0.30), residues: 294 sheet: -0.55 (0.33), residues: 248 loop : -1.01 (0.26), residues: 588 *********************** 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 218 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 198 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 205 average time/residue: 0.2235 time to fit residues: 63.3731 Evaluate side-chains 176 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0962 time to fit residues: 3.5968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 581 ASN B 111 GLN ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** 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: 0.6503 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 9634 Z= 0.352 Angle : 0.696 7.214 13016 Z= 0.361 Chirality : 0.048 0.191 1441 Planarity : 0.005 0.055 1665 Dihedral : 5.294 22.460 1246 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 2.84 % 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: -0.76 (0.25), residues: 1130 helix: 0.72 (0.30), residues: 289 sheet: -0.67 (0.34), residues: 227 loop : -1.01 (0.25), residues: 614 *********************** 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 213 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 12 residues processed: 197 average time/residue: 0.2201 time to fit residues: 60.5845 Evaluate side-chains 172 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 160 time to evaluate : 1.027 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1285 time to fit residues: 3.9075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 29 optimal weight: 0.0980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 581 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 9634 Z= 0.310 Angle : 0.653 7.770 13016 Z= 0.340 Chirality : 0.047 0.194 1441 Planarity : 0.005 0.052 1665 Dihedral : 5.190 21.801 1246 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 2.37 % 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: -0.85 (0.25), residues: 1130 helix: 0.70 (0.30), residues: 297 sheet: -0.78 (0.34), residues: 227 loop : -1.09 (0.25), residues: 606 *********************** 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 197 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 172 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 185 average time/residue: 0.2069 time to fit residues: 54.5587 Evaluate side-chains 164 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0945 time to fit residues: 3.4900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 0.5980 chunk 98 optimal weight: 0.2980 chunk 27 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 581 ASN A 582 ASN A1024 GLN A1275 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 9634 Z= 0.195 Angle : 0.599 7.702 13016 Z= 0.310 Chirality : 0.045 0.165 1441 Planarity : 0.005 0.065 1665 Dihedral : 4.919 19.548 1246 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 1.80 % 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: -0.61 (0.25), residues: 1130 helix: 0.93 (0.30), residues: 297 sheet: -0.70 (0.34), residues: 231 loop : -0.94 (0.26), residues: 602 *********************** 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 185 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 166 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 173 average time/residue: 0.2029 time to fit residues: 50.8961 Evaluate side-chains 160 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 1.180 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0930 time to fit residues: 2.8092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.0970 chunk 99 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 0.0040 chunk 110 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.0980 chunk 57 optimal weight: 0.8980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN 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: 0.6403 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9634 Z= 0.176 Angle : 0.580 7.872 13016 Z= 0.301 Chirality : 0.044 0.161 1441 Planarity : 0.005 0.058 1665 Dihedral : 4.693 19.596 1246 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 1.42 % 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: -0.47 (0.25), residues: 1130 helix: 1.15 (0.30), residues: 295 sheet: -0.75 (0.33), residues: 242 loop : -0.83 (0.26), residues: 593 *********************** 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 181 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 174 average time/residue: 0.2021 time to fit residues: 50.3968 Evaluate side-chains 158 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 152 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0913 time to fit residues: 2.5991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN C 217 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 9634 Z= 0.314 Angle : 0.644 8.039 13016 Z= 0.336 Chirality : 0.046 0.218 1441 Planarity : 0.005 0.054 1665 Dihedral : 4.983 19.650 1246 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 2.27 % 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: -0.72 (0.25), residues: 1130 helix: 0.98 (0.30), residues: 308 sheet: -0.96 (0.33), residues: 239 loop : -1.03 (0.26), residues: 583 *********************** 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 180 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 168 average time/residue: 0.2157 time to fit residues: 51.2074 Evaluate side-chains 157 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 148 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0992 time to fit residues: 3.1493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 10 optimal weight: 0.0270 chunk 86 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 0.0670 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 581 ASN ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 9634 Z= 0.186 Angle : 0.618 10.519 13016 Z= 0.321 Chirality : 0.045 0.207 1441 Planarity : 0.005 0.053 1665 Dihedral : 4.765 19.998 1246 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 1.04 % 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: -0.61 (0.25), residues: 1130 helix: 1.03 (0.30), residues: 308 sheet: -1.00 (0.34), residues: 220 loop : -0.90 (0.25), residues: 602 *********************** 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 170 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 164 average time/residue: 0.2226 time to fit residues: 51.7452 Evaluate side-chains 154 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0927 time to fit residues: 2.3821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN A 680 GLN A1075 ASN B 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 9634 Z= 0.329 Angle : 0.679 7.743 13016 Z= 0.354 Chirality : 0.047 0.251 1441 Planarity : 0.005 0.058 1665 Dihedral : 5.066 21.581 1246 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 1.04 % 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: -0.71 (0.25), residues: 1130 helix: 0.99 (0.30), residues: 302 sheet: -0.92 (0.34), residues: 222 loop : -1.03 (0.25), residues: 606 *********************** 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 162 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 155 average time/residue: 0.1959 time to fit residues: 43.8837 Evaluate side-chains 148 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1004 time to fit residues: 2.6008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.0370 chunk 75 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN B 111 GLN C 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.5144 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= 0.228 Angle : 0.650 11.611 13016 Z= 0.333 Chirality : 0.045 0.178 1441 Planarity : 0.005 0.057 1665 Dihedral : 4.875 19.871 1246 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 0.47 % 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: -0.61 (0.25), residues: 1130 helix: 1.06 (0.30), residues: 297 sheet: -0.92 (0.33), residues: 230 loop : -0.91 (0.26), residues: 603 ********************** 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 157 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 154 average time/residue: 0.2002 time to fit residues: 44.6413 Evaluate side-chains 150 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 148 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0871 time to fit residues: 1.8976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.0970 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 93 optimal weight: 0.1980 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.204739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.164479 restraints weight = 14930.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.166820 restraints weight = 8306.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.168708 restraints weight = 6260.784| |-----------------------------------------------------------------------------| r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9634 Z= 0.222 Angle : 0.639 10.531 13016 Z= 0.329 Chirality : 0.045 0.166 1441 Planarity : 0.005 0.055 1665 Dihedral : 4.814 23.208 1246 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.47 % 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: -0.67 (0.25), residues: 1130 helix: 0.92 (0.30), residues: 308 sheet: -0.95 (0.33), residues: 235 loop : -0.92 (0.26), residues: 587 =============================================================================== Job complete usr+sys time: 2066.72 seconds wall clock time: 38 minutes 19.86 seconds (2299.86 seconds total)