Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 12:54:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/10_2023/7dfl_30665_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/10_2023/7dfl_30665.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/10_2023/7dfl_30665_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/10_2023/7dfl_30665_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/10_2023/7dfl_30665_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/10_2023/7dfl_30665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/10_2023/7dfl_30665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/10_2023/7dfl_30665_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dfl_30665/10_2023/7dfl_30665_neut_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.078 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 66 5.16 5 C 5729 2.51 5 N 1535 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 153": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 8987 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2273 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 9, 'TRANS': 265} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "A" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1847 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain breaks: 2 Chain: "C" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1808 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.10, per 1000 atoms: 0.57 Number of scatterers: 8987 At special positions: 0 Unit cell: (90.72, 119.88, 126.36, 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 66 16.00 O 1657 8.00 N 1535 7.00 C 5729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 180 " distance=2.04 Simple disulfide: pdb=" SG CYS R 441 " - pdb=" SG CYS R 444 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 229 " distance=1.95 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: 3.30 Conformation dependent library (CDL) restraints added in 1.4 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 13 sheets defined 33.5% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'R' and resid 29 through 52 Processing helix chain 'R' and resid 61 through 79 removed outlier: 4.084A pdb=" N TYR R 65 " --> pdb=" O VAL R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 89 Processing helix chain 'R' and resid 97 through 130 Processing helix chain 'R' and resid 141 through 163 removed outlier: 4.816A pdb=" N TRP R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL R 159 " --> pdb=" O SER R 155 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ILE R 160 " --> pdb=" O PHE R 156 " (cutoff:3.500A) Proline residue: R 161 - end of helix Processing helix chain 'R' and resid 169 through 171 No H-bonds generated for 'chain 'R' and resid 169 through 171' Processing helix chain 'R' and resid 188 through 198 Processing helix chain 'R' and resid 200 through 217 Processing helix chain 'R' and resid 409 through 438 Proline residue: R 430 - end of helix removed outlier: 3.735A pdb=" N PHE R 434 " --> pdb=" O PRO R 430 " (cutoff:3.500A) Processing helix chain 'R' and resid 446 through 466 removed outlier: 3.586A pdb=" N ASN R 460 " --> pdb=" O LEU R 456 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER R 461 " --> pdb=" O GLY R 457 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR R 462 " --> pdb=" O TYR R 458 " (cutoff:3.500A) Proline residue: R 465 - end of helix Processing helix chain 'R' and resid 469 through 471 No H-bonds generated for 'chain 'R' and resid 469 through 471' Processing helix chain 'R' and resid 476 through 481 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'A' and resid 7 through 36 removed outlier: 4.128A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 247 through 259 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 277 through 283 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 336 through 355 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 53 through 55 No H-bonds generated for 'chain 'C' and resid 53 through 55' Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.970A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.047A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.861A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.847A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 240 through 245 removed outlier: 4.086A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 276 through 278 Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.936A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 268 through 274 removed outlier: 4.112A pdb=" N SER A 225 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE A 200 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N LEU A 42 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG A 202 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU A 44 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 204 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'C' and resid 115 through 117 removed outlier: 5.827A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ALA C 40 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU C 45 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'C' and resid 146 through 149 removed outlier: 7.459A pdb=" N LYS C 244 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL C 149 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU C 246 " --> pdb=" O VAL C 149 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 226 through 231 removed outlier: 6.055A pdb=" N LEU C 178 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU C 187 " --> pdb=" O LEU C 178 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1098 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2897 1.35 - 1.47: 2300 1.47 - 1.59: 3884 1.59 - 1.71: 0 1.71 - 1.84: 100 Bond restraints: 9181 Sorted by residual: bond pdb=" C VAL R 80 " pdb=" O VAL R 80 " ideal model delta sigma weight residual 1.233 1.285 -0.052 1.02e-02 9.61e+03 2.60e+01 bond pdb=" N THR C 118 " pdb=" CA THR C 118 " ideal model delta sigma weight residual 1.457 1.509 -0.052 1.23e-02 6.61e+03 1.76e+01 bond pdb=" N PRO C 236 " pdb=" CD PRO C 236 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 bond pdb=" N LEU C 187 " pdb=" CA LEU C 187 " ideal model delta sigma weight residual 1.456 1.503 -0.046 1.22e-02 6.72e+03 1.44e+01 bond pdb=" N VAL R 80 " pdb=" CA VAL R 80 " ideal model delta sigma weight residual 1.454 1.497 -0.043 1.19e-02 7.06e+03 1.30e+01 ... (remaining 9176 not shown) Histogram of bond angle deviations from ideal: 96.80 - 104.25: 118 104.25 - 111.70: 4235 111.70 - 119.14: 3207 119.14 - 126.59: 4731 126.59 - 134.04: 136 Bond angle restraints: 12427 Sorted by residual: angle pdb=" N ARG R 218 " pdb=" CA ARG R 218 " pdb=" C ARG R 218 " ideal model delta sigma weight residual 110.80 121.85 -11.05 2.13e+00 2.20e-01 2.69e+01 angle pdb=" N SER C 136 " pdb=" CA SER C 136 " pdb=" C SER C 136 " ideal model delta sigma weight residual 110.80 100.47 10.33 2.13e+00 2.20e-01 2.35e+01 angle pdb=" N ARG R 134 " pdb=" CA ARG R 134 " pdb=" C ARG R 134 " ideal model delta sigma weight residual 108.58 99.99 8.59 1.82e+00 3.02e-01 2.23e+01 angle pdb=" N HIS R 406 " pdb=" CA HIS R 406 " pdb=" C HIS R 406 " ideal model delta sigma weight residual 108.02 116.30 -8.28 1.78e+00 3.16e-01 2.16e+01 angle pdb=" N CYS R 445 " pdb=" CA CYS R 445 " pdb=" C CYS R 445 " ideal model delta sigma weight residual 110.80 101.30 9.50 2.13e+00 2.20e-01 1.99e+01 ... (remaining 12422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 5047 16.82 - 33.65: 340 33.65 - 50.47: 54 50.47 - 67.29: 9 67.29 - 84.12: 6 Dihedral angle restraints: 5456 sinusoidal: 2161 harmonic: 3295 Sorted by residual: dihedral pdb=" C SER C 136 " pdb=" N SER C 136 " pdb=" CA SER C 136 " pdb=" CB SER C 136 " ideal model delta harmonic sigma weight residual -122.60 -110.84 -11.76 0 2.50e+00 1.60e-01 2.21e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 160.04 19.96 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ARG R 134 " pdb=" C ARG R 134 " pdb=" N TYR R 135 " pdb=" CA TYR R 135 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 5453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1233 0.085 - 0.169: 142 0.169 - 0.254: 14 0.254 - 0.339: 2 0.339 - 0.423: 2 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA SER C 136 " pdb=" N SER C 136 " pdb=" C SER C 136 " pdb=" CB SER C 136 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA SER B 67 " pdb=" N SER B 67 " pdb=" C SER B 67 " pdb=" CB SER B 67 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA ARG R 218 " pdb=" N ARG R 218 " pdb=" C ARG R 218 " pdb=" CB ARG R 218 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1390 not shown) Planarity restraints: 1568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 235 " 0.061 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO C 236 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 435 " -0.029 2.00e-02 2.50e+03 2.46e-02 1.06e+01 pdb=" CG PHE R 435 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE R 435 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE R 435 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE R 435 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 435 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE R 435 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 234 " -0.025 2.00e-02 2.50e+03 2.02e-02 7.15e+00 pdb=" CG PHE B 234 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 234 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 234 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 234 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 234 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 234 " -0.004 2.00e-02 2.50e+03 ... (remaining 1565 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 34 2.51 - 3.11: 7019 3.11 - 3.70: 13399 3.70 - 4.30: 19462 4.30 - 4.90: 32443 Nonbonded interactions: 72357 Sorted by model distance: nonbonded pdb=" SD MET A 203 " pdb=" CE MET A 227 " model vdw 1.910 3.820 nonbonded pdb=" O ILE B 43 " pdb=" NH2 ARG B 304 " model vdw 2.129 2.520 nonbonded pdb=" O ILE R 37 " pdb=" OG1 THR R 41 " model vdw 2.165 2.440 nonbonded pdb=" OG SER B 227 " pdb=" OD1 ASP B 247 " model vdw 2.186 2.440 nonbonded pdb=" OD2 ASP B 212 " pdb=" N GLU B 215 " model vdw 2.297 2.520 ... (remaining 72352 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 3.850 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 26.580 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 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 : 0.008 0.072 9181 Z= 0.503 Angle : 0.950 11.046 12427 Z= 0.557 Chirality : 0.057 0.423 1393 Planarity : 0.006 0.089 1568 Dihedral : 11.967 84.118 3318 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.24), residues: 1115 helix: 0.54 (0.27), residues: 363 sheet: -0.92 (0.32), residues: 252 loop : -1.31 (0.26), residues: 500 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.2479 time to fit residues: 111.4730 Evaluate side-chains 223 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9181 Z= 0.212 Angle : 0.656 8.122 12427 Z= 0.336 Chirality : 0.044 0.172 1393 Planarity : 0.005 0.062 1568 Dihedral : 5.348 42.918 1238 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.24 % Allowed : 13.43 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.25), residues: 1115 helix: 1.11 (0.27), residues: 366 sheet: -0.46 (0.33), residues: 240 loop : -0.99 (0.27), residues: 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 253 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 267 average time/residue: 0.2238 time to fit residues: 81.2420 Evaluate side-chains 226 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 211 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0885 time to fit residues: 3.8182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 83 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 131 GLN G 18 GLN ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9181 Z= 0.180 Angle : 0.637 9.907 12427 Z= 0.325 Chirality : 0.043 0.151 1393 Planarity : 0.004 0.076 1568 Dihedral : 4.985 41.043 1238 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.75 % Allowed : 14.65 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.09 (0.25), residues: 1115 helix: 1.15 (0.27), residues: 361 sheet: -0.32 (0.33), residues: 238 loop : -0.74 (0.27), residues: 516 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 239 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 251 average time/residue: 0.2213 time to fit residues: 75.7295 Evaluate side-chains 224 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 207 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0930 time to fit residues: 4.2108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.7980 chunk 75 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 67 optimal weight: 0.0000 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 75 GLN A 197 GLN ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9181 Z= 0.185 Angle : 0.618 9.573 12427 Z= 0.320 Chirality : 0.043 0.160 1393 Planarity : 0.004 0.069 1568 Dihedral : 4.764 37.958 1238 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.73 % Allowed : 16.99 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.25), residues: 1115 helix: 1.26 (0.27), residues: 363 sheet: -0.38 (0.32), residues: 245 loop : -0.70 (0.28), residues: 507 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 229 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 237 average time/residue: 0.2174 time to fit residues: 70.9373 Evaluate side-chains 212 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 202 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0873 time to fit residues: 3.0120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9181 Z= 0.304 Angle : 0.664 9.190 12427 Z= 0.345 Chirality : 0.045 0.167 1393 Planarity : 0.004 0.070 1568 Dihedral : 4.876 34.986 1238 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.54 % Allowed : 17.50 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.25), residues: 1115 helix: 1.38 (0.26), residues: 361 sheet: -0.51 (0.31), residues: 252 loop : -0.81 (0.28), residues: 502 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 208 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 218 average time/residue: 0.2300 time to fit residues: 67.7650 Evaluate side-chains 209 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 195 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0971 time to fit residues: 3.8433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9181 Z= 0.199 Angle : 0.644 11.854 12427 Z= 0.330 Chirality : 0.043 0.138 1393 Planarity : 0.004 0.065 1568 Dihedral : 4.716 32.804 1238 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.12 % Allowed : 18.51 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.25), residues: 1115 helix: 1.46 (0.26), residues: 361 sheet: -0.51 (0.31), residues: 253 loop : -0.78 (0.28), residues: 501 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 215 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 218 average time/residue: 0.2165 time to fit residues: 64.8017 Evaluate side-chains 207 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 203 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1054 time to fit residues: 2.1230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9181 Z= 0.284 Angle : 0.675 10.256 12427 Z= 0.351 Chirality : 0.044 0.144 1393 Planarity : 0.005 0.070 1568 Dihedral : 4.775 32.613 1238 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.42 % Allowed : 19.63 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.25), residues: 1115 helix: 1.34 (0.26), residues: 361 sheet: -0.58 (0.31), residues: 253 loop : -0.80 (0.28), residues: 501 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 206 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 212 average time/residue: 0.2218 time to fit residues: 64.5011 Evaluate side-chains 200 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 192 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1015 time to fit residues: 2.8671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 472 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9181 Z= 0.256 Angle : 0.687 11.045 12427 Z= 0.354 Chirality : 0.044 0.160 1393 Planarity : 0.004 0.066 1568 Dihedral : 4.742 32.030 1238 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.61 % Allowed : 21.06 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.25), residues: 1115 helix: 1.34 (0.27), residues: 357 sheet: -0.58 (0.31), residues: 252 loop : -0.84 (0.28), residues: 506 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 201 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 204 average time/residue: 0.2242 time to fit residues: 62.5694 Evaluate side-chains 195 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 190 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0859 time to fit residues: 2.1361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 0.0770 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9181 Z= 0.230 Angle : 0.671 10.840 12427 Z= 0.345 Chirality : 0.044 0.165 1393 Planarity : 0.004 0.066 1568 Dihedral : 4.709 31.765 1238 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.41 % Allowed : 20.75 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.25), residues: 1115 helix: 1.29 (0.27), residues: 358 sheet: -0.55 (0.31), residues: 253 loop : -0.86 (0.28), residues: 504 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 216 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 217 average time/residue: 0.2260 time to fit residues: 67.0798 Evaluate side-chains 191 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0868 time to fit residues: 1.6140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 100 optimal weight: 0.3980 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9181 Z= 0.213 Angle : 0.681 11.310 12427 Z= 0.349 Chirality : 0.044 0.180 1393 Planarity : 0.004 0.065 1568 Dihedral : 4.699 39.972 1238 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.20 % Allowed : 22.58 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.25), residues: 1115 helix: 1.39 (0.27), residues: 354 sheet: -0.55 (0.32), residues: 243 loop : -0.74 (0.27), residues: 518 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 192 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 193 average time/residue: 0.2206 time to fit residues: 58.8198 Evaluate side-chains 186 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 1.051 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0928 time to fit residues: 1.6313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.146423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.109316 restraints weight = 14887.145| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 3.96 r_work: 0.3330 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9181 Z= 0.260 Angle : 0.681 10.910 12427 Z= 0.352 Chirality : 0.045 0.195 1393 Planarity : 0.004 0.067 1568 Dihedral : 4.714 35.246 1238 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.10 % Allowed : 22.79 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.25), residues: 1115 helix: 1.27 (0.27), residues: 356 sheet: -0.59 (0.31), residues: 242 loop : -0.81 (0.27), residues: 517 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2308.13 seconds wall clock time: 42 minutes 34.83 seconds (2554.83 seconds total)