Starting phenix.real_space_refine on Sun May 19 16:32:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7un3_26612.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7un3_26612.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global c_beta_restraints=False ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True resolution=3.5 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7un3_26612.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7un3_26612.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7un3_26612.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7un3_26612.map" } resolution = 3.5 refinement { run = *minimization_global rigid_body local_grid_search morphing \ simulated_annealing adp occupancy nqh_flips } pdb_interpretation { c_beta_restraints = False ramachandran_plot_restraints { enabled = False } } 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= 0.026 sd= 0.153 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: 5 Type Number sf(0) Gaussians S 41 5.16 5 C 6056 2.51 5 N 1605 2.21 5 O 1738 1.98 5 H 9482 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1256": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 18922 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1193 Classifications: {'peptide': 73} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "A" Number of atoms: 10424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 10424 Inner-chain residues flagged as termini: ['pdbres="HIS A 83 "', 'pdbres="VAL A 122 "', 'pdbres="TYR A 241 "', 'pdbres="PHE A 260 "', 'pdbres="PHE A 313 "', 'pdbres="VAL A 321 "', 'pdbres="LEU A 339 "', 'pdbres="ASP A 343 "', 'pdbres="PRO A 358 "', 'pdbres="ASP A 542 "', 'pdbres="GLY A 663 "', 'pdbres="GLU A 675 "', 'pdbres="ILE A 710 "', 'pdbres="VAL A 928 "', 'pdbres="THR A1046 "', 'pdbres="ARG A1054 "', 'pdbres="LEU A1152 "', 'pdbres="PRO A1252 "'] Classifications: {'peptide': 649} Modifications used: {'COO': 10, 'NH2': 1, 'NH3': 9} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 611} Chain breaks: 9 Chain: "B" Number of atoms: 3686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3686 Inner-chain residues flagged as termini: ['pdbres="ILE B 121 "', 'pdbres="PRO B 164 "', 'pdbres="VAL B 306 "', 'pdbres="ILE B 319 "'] Classifications: {'peptide': 223} Modifications used: {'COO': 3, 'NH2': 1, 'NH3': 2} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain breaks: 2 Chain: "C" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3619 Inner-chain residues flagged as termini: ['pdbres="ASN C 122 "', 'pdbres="GLY C 166 "', 'pdbres="VAL C 306 "', 'pdbres="ASP C 315 "'] Classifications: {'peptide': 219} Modifications used: {'COO': 3, 'NH3': 3} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain breaks: 2 Time building chain proxies: 5.41, per 1000 atoms: 0.29 Number of scatterers: 18922 At special positions: 0 Unit cell: (84.975, 114.675, 142.725, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 O 1738 8.00 N 1605 7.00 C 6056 6.00 H 9482 1.00 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: 8.87 Conformation dependent library (CDL) restraints added in 1.3 seconds Finding SS restraints... Secondary structure from input PDB file: 34 helices and 17 sheets defined 29.7% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'D' and resid 23 through 34 Processing helix chain 'D' and resid 38 through 40 No H-bonds generated for 'chain 'D' and resid 38 through 40' Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 234 through 239 removed outlier: 5.001A pdb=" N LYS A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 330 through 335 removed outlier: 4.360A pdb=" N GLY A 334 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A 335 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 951 through 967 removed outlier: 3.579A pdb=" N LYS A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1044 No H-bonds generated for 'chain 'A' and resid 1042 through 1044' Processing helix chain 'A' and resid 1061 through 1070 Processing helix chain 'A' and resid 1077 through 1080 Processing helix chain 'A' and resid 1085 through 1087 No H-bonds generated for 'chain 'A' and resid 1085 through 1087' Processing helix chain 'A' and resid 1091 through 1117 Processing helix chain 'A' and resid 1124 through 1132 Processing helix chain 'A' and resid 1135 through 1151 removed outlier: 3.917A pdb=" N VAL A1139 " --> pdb=" O GLY A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1282 removed outlier: 3.775A pdb=" N GLN A1275 " --> pdb=" O GLY A1271 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 120 removed outlier: 3.961A pdb=" N VAL B 108 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 4.122A 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 170 through 176 Processing helix chain 'B' and resid 179 through 184 removed outlier: 4.479A pdb=" N MET B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 Proline residue: B 191 - end of helix removed outlier: 4.391A pdb=" N HIS B 195 " --> pdb=" O PRO B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 320 through 332 Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'C' and resid 74 through 121 Proline residue: C 112 - end of helix Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 179 through 182 No H-bonds generated for 'chain 'C' and resid 179 through 182' Processing helix chain 'C' and resid 187 through 195 Proline residue: C 191 - end of helix removed outlier: 4.527A pdb=" N LYS C 194 " --> pdb=" O PRO C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 302 removed outlier: 4.186A pdb=" N PHE C 300 " --> pdb=" O PHE C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 332 Processing helix chain 'C' and resid 339 through 341 No H-bonds generated for 'chain 'C' and resid 339 through 341' Processing sheet with id= A, first strand: chain 'D' and resid 12 through 16 removed outlier: 6.172A pdb=" N SER D 65 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LYS D 6 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU D 67 " --> pdb=" O LYS D 6 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 141 through 144 removed outlier: 6.715A pdb=" N LEU A 65 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG A 123 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 573 through 575 Processing sheet with id= D, first strand: chain 'A' and resid 169 through 171 Processing sheet with id= E, first strand: chain 'A' and resid 175 through 177 Processing sheet with id= F, first strand: chain 'A' and resid 265 through 269 removed outlier: 6.798A pdb=" N SER A 231 " --> pdb=" O TRP A 278 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N TRP A 278 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 590 through 592 Processing sheet with id= H, first strand: chain 'A' and resid 707 through 709 removed outlier: 7.075A pdb=" N GLU A 691 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 974 through 977 Processing sheet with id= J, first strand: chain 'A' and resid 209 through 213 removed outlier: 4.020A pdb=" N THR A 310 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LYS A 212 " --> pdb=" O TRP A 308 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TRP A 308 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 215 through 221 removed outlier: 3.593A pdb=" N ASP A 215 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLN A 219 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL A 301 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 221 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL A 299 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 604 through 611 removed outlier: 6.916A pdb=" N MET A 618 " --> pdb=" O GLN A 608 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY A 610 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR A 616 " --> pdb=" O GLY A 610 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYS A 623 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU A 633 " --> pdb=" O LYS A 623 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 228 through 232 removed outlier: 3.988A pdb=" N LYS B 231 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 214 " --> pdb=" O LYS B 231 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 270 through 278 Processing sheet with id= O, first strand: chain 'B' and resid 233 through 235 removed outlier: 3.694A pdb=" N GLY B 254 " --> pdb=" O ARG B 234 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 228 through 234 Processing sheet with id= Q, first strand: chain 'C' and resid 270 through 278 327 hydrogen bonds defined for protein. 927 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: 7.19 Time building geometry restraints manager: 8.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 9462 1.15 - 1.31: 1597 1.31 - 1.48: 3812 1.48 - 1.65: 4200 1.65 - 1.82: 62 Bond restraints: 19133 Sorted by residual: bond pdb=" N CYS A1025 " pdb=" H CYS A1025 " ideal model delta sigma weight residual 0.860 1.027 -0.167 2.00e-02 2.50e+03 6.94e+01 bond pdb=" N ASP A 144 " pdb=" H ASP A 144 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" N ARG B 337 " pdb=" H ARG B 337 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.72e+01 bond pdb=" N GLU A1081 " pdb=" H GLU A1081 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" N ASP A 151 " pdb=" H ASP A 151 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.64e+01 ... (remaining 19128 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.99: 422 106.99 - 113.74: 22868 113.74 - 120.50: 6186 120.50 - 127.25: 5082 127.25 - 134.01: 112 Bond angle restraints: 34670 Sorted by residual: angle pdb=" C ALA A 695 " pdb=" CA ALA A 695 " pdb=" CB ALA A 695 " ideal model delta sigma weight residual 117.23 111.62 5.61 1.36e+00 5.41e-01 1.70e+01 angle pdb=" CA ALA A 695 " pdb=" C ALA A 695 " pdb=" N ASP A 696 " ideal model delta sigma weight residual 119.98 117.43 2.55 8.50e-01 1.38e+00 9.00e+00 angle pdb=" N GLN B 111 " pdb=" CA GLN B 111 " pdb=" C GLN B 111 " ideal model delta sigma weight residual 109.81 114.20 -4.39 2.21e+00 2.05e-01 3.95e+00 angle pdb=" CA GLN B 111 " pdb=" C GLN B 111 " pdb=" N PRO B 112 " ideal model delta sigma weight residual 118.44 121.37 -2.93 1.59e+00 3.96e-01 3.39e+00 angle pdb=" N ASN A 581 " pdb=" CA ASN A 581 " pdb=" CB ASN A 581 " ideal model delta sigma weight residual 114.27 111.25 3.02 1.64e+00 3.72e-01 3.39e+00 ... (remaining 34665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 5958 17.29 - 34.58: 571 34.58 - 51.87: 172 51.87 - 69.16: 46 69.16 - 86.45: 8 Dihedral angle restraints: 6755 sinusoidal: 4897 harmonic: 1858 Sorted by residual: 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 -163.31 -16.69 0 5.00e+00 4.00e-02 1.11e+01 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 -163.32 -16.68 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CG LYS A 217 " pdb=" CD LYS A 217 " pdb=" CE LYS A 217 " pdb=" NZ LYS A 217 " ideal model delta sinusoidal sigma weight residual 180.00 124.91 55.09 3 1.50e+01 4.44e-03 9.33e+00 ... (remaining 6752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 924 0.031 - 0.061: 306 0.061 - 0.092: 114 0.092 - 0.123: 81 0.123 - 0.154: 16 Chirality restraints: 1441 Sorted by residual: 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 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA ILE A 660 " pdb=" N ILE A 660 " pdb=" C ILE A 660 " pdb=" CB ILE A 660 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE B 199 " pdb=" N ILE B 199 " pdb=" C ILE B 199 " pdb=" CB ILE B 199 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 1438 not shown) Planarity restraints: 2768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 111 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO B 112 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1256 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.13e+00 pdb=" N PRO A1257 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A1257 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1257 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 190 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO B 191 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 191 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 191 " 0.022 5.00e-02 4.00e+02 ... (remaining 2765 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 808 2.05 - 2.69: 27710 2.69 - 3.32: 56366 3.32 - 3.96: 73278 3.96 - 4.60: 108242 Nonbonded interactions: 266404 Sorted by model distance: nonbonded pdb=" HH TYR A 643 " pdb=" OE1 GLU A1102 " model vdw 1.412 1.850 nonbonded pdb=" O TYR A 203 " pdb=" H LEU A 339 " model vdw 1.413 1.850 nonbonded pdb=" H GLY A 263 " pdb=" O VAL A 296 " model vdw 1.481 1.850 nonbonded pdb=" OD1 ASN C 226 " pdb=" H ASP C 261 " model vdw 1.487 1.850 nonbonded pdb=" O VAL B 178 " pdb=" H SER B 182 " model vdw 1.502 1.850 ... (remaining 266399 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 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB or name CG1 or name CG2 or name CD1 or name H or name H \ A or name HB or name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or \ name HD11 or name HD12 or name HD13)) or (resid 166 and (name N or name CA or n \ ame C or name O or name HA2 or name HA3)) or resid 167 through 187 or (resid 188 \ and (name N or name CA or name C or name O or name CB or name CG or name ND1 or \ name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 o \ r name HD1 or name HD2 or name HE1)) or resid 189 through 306 or (resid 319 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2 or nam \ e CD1 or name HA or name HB or name HG12 or name HG13 or name HG21 or name HG22 \ or name HG23 or name HD11 or name HD12 or name HD13)) or resid 320 through 342)) \ selection = (chain 'C' and (resid 73 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 101 through 121 or (resid 166 and (name N or name CA or name C or \ name O or name HA2 or name HA3)) or resid 167 through 306 or (resid 319 and (na \ me N or name CA or name C or name O or name CB or name CG1 or name CG2 or name C \ D1 or name HA or name HB or name HG12 or name HG13 or name HG21 or name HG22 or \ name HG23 or name HD11 or name HD12 or name HD13)) or resid 320 through 341 or ( \ resid 342 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H or name HA or na \ me HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name HZ )) \ )) } 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: 5 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.50 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will not be refined Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 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: 0.180 Extract box with map and model: 0.450 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 36.160 Find NCS groups from input model: 0.320 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:0.000 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:25.600 Internal consistency checks: 0.000 Total: 62.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 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 : 0.002 0.026 9651 Z= 0.159 Angle : 0.528 5.608 13050 Z= 0.283 Chirality : 0.043 0.154 1441 Planarity : 0.004 0.046 1682 Dihedral : 12.824 86.452 3630 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.09 % Allowed : 1.89 % Favored : 98.01 % 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: -1.42 (0.24), residues: 1130 helix: 0.05 (0.28), residues: 308 sheet: -0.86 (0.32), residues: 248 loop : -1.51 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.013 0.001 TYR A1100 PHE 0.011 0.001 PHE A 622 TRP 0.008 0.001 TRP B 171 HIS 0.004 0.001 HIS B 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 9651 Z= 0.382 Angle : 0.650 7.082 13050 Z= 0.345 Chirality : 0.060 0.245 1441 Planarity : 0.005 0.055 1682 Dihedral : 12.263 85.090 3630 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.88 % Allowed : 10.53 % Favored : 88.58 % Rotamer: Outliers : 0.28 % Allowed : 2.56 % Favored : 97.16 % 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: -3.06 (0.22), residues: 1130 helix: -0.96 (0.26), residues: 297 sheet: -1.65 (0.32), residues: 236 loop : -2.84 (0.22), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1088 TYR 0.012 0.002 TYR B 233 PHE 0.028 0.002 PHE B 212 TRP 0.012 0.001 TRP A 278 HIS 0.007 0.001 HIS C 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 overall best weight: 9.3996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 9651 Z= 0.461 Angle : 0.689 6.718 13050 Z= 0.370 Chirality : 0.064 0.212 1441 Planarity : 0.006 0.052 1682 Dihedral : 12.852 84.237 3630 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 2.65 % Allowed : 13.63 % Favored : 83.72 % Rotamer: Outliers : 1.99 % Allowed : 5.21 % Favored : 92.80 % 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: -4.41 (0.20), residues: 1130 helix: -1.64 (0.25), residues: 287 sheet: -2.30 (0.30), residues: 235 loop : -4.01 (0.20), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 293 TYR 0.024 0.002 TYR B 233 PHE 0.026 0.002 PHE B 212 TRP 0.021 0.002 TRP A 278 HIS 0.006 0.001 HIS A 706 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 79 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9651 Z= 0.310 Angle : 0.570 6.109 13050 Z= 0.303 Chirality : 0.059 0.195 1441 Planarity : 0.005 0.045 1682 Dihedral : 12.344 82.157 3630 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 1.95 % Allowed : 11.42 % Favored : 86.64 % Rotamer: Outliers : 1.42 % Allowed : 5.11 % Favored : 93.47 % 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: -4.27 (0.20), residues: 1130 helix: -1.67 (0.24), residues: 297 sheet: -2.38 (0.29), residues: 246 loop : -3.80 (0.20), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 569 TYR 0.013 0.001 TYR B 233 PHE 0.022 0.002 PHE B 212 TRP 0.015 0.001 TRP A 278 HIS 0.005 0.001 HIS C 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 10.0000 chunk 108 optimal weight: 40.0000 chunk 87 optimal weight: 70.0000 chunk 42 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 71 optimal weight: 30.0000 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 overall best weight: 9.1996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 9651 Z= 0.448 Angle : 0.688 6.256 13050 Z= 0.373 Chirality : 0.064 0.222 1441 Planarity : 0.006 0.068 1682 Dihedral : 13.022 78.942 3630 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 26.18 Ramachandran Plot: Outliers : 4.34 % Allowed : 15.84 % Favored : 79.82 % Rotamer: Outliers : 2.65 % Allowed : 7.48 % Favored : 89.87 % 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: -5.22 (0.19), residues: 1130 helix: -2.34 (0.23), residues: 289 sheet: -2.78 (0.30), residues: 241 loop : -4.53 (0.18), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 293 TYR 0.018 0.002 TYR B 233 PHE 0.024 0.002 PHE B 212 TRP 0.023 0.002 TRP A 278 HIS 0.006 0.001 HIS A 706 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 81 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 110 optimal weight: 50.0000 chunk 66 optimal weight: 30.0000 chunk 33 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 1 optimal weight: 50.0000 overall best weight: 11.1996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 9651 Z= 0.470 Angle : 0.672 6.448 13050 Z= 0.367 Chirality : 0.062 0.247 1441 Planarity : 0.006 0.068 1682 Dihedral : 13.346 75.048 3630 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 24.22 Ramachandran Plot: Outliers : 4.25 % Allowed : 16.28 % Favored : 79.47 % Rotamer: Outliers : 2.94 % Allowed : 8.71 % Favored : 88.35 % 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: -5.33 (0.19), residues: 1130 helix: -2.50 (0.23), residues: 289 sheet: -3.17 (0.30), residues: 215 loop : -4.38 (0.18), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 154 TYR 0.013 0.002 TYR A1100 PHE 0.028 0.002 PHE B 212 TRP 0.021 0.002 TRP A 278 HIS 0.005 0.001 HIS A 706 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 409.32 seconds wall clock time: 7 minutes 53.04 seconds (473.04 seconds total)