Starting phenix.real_space_refine on Thu Jul 2 11:07:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yud_34104/07_2026/7yud_34104_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yud_34104/07_2026/7yud_34104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yud_34104/07_2026/7yud_34104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yud_34104/07_2026/7yud_34104.map" model { file = "/net/cci-nas-00/data/ceres_data/7yud_34104/07_2026/7yud_34104_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yud_34104/07_2026/7yud_34104_neut.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.132 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 P 1 5.49 5 S 41 5.16 5 C 5391 2.51 5 N 1410 2.21 5 O 1598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8441 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1732 Classifications: {'peptide': 229} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 217} Chain: "L" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1619 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "N" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 959 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "R" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3183 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 12, 'TRANS': 404} Chain breaks: 2 Chain: "K" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'J89': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.85, per 1000 atoms: 0.22 Number of scatterers: 8441 At special positions: 0 Unit cell: (82.5, 88, 162.8, 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 P 1 15.00 O 1598 8.00 N 1410 7.00 C 5391 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 26 " - pdb=" SG CYS H 100 " distance=2.05 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 215 " distance=2.04 Simple disulfide: pdb=" SG CYS L 25 " - pdb=" SG CYS L 90 " distance=2.05 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 97 " distance=2.05 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.59 Conformation dependent library (CDL) restraints added in 480.3 milliseconds 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 16 sheets defined 37.6% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'H' and resid 32 through 36 removed outlier: 3.981A pdb=" N TYR H 36 " --> pdb=" O PHE H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 95 removed outlier: 3.979A pdb=" N THR H 95 " --> pdb=" O ALA H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 175 through 177 No H-bonds generated for 'chain 'H' and resid 175 through 177' Processing helix chain 'H' and resid 206 through 210 Processing helix chain 'L' and resid 123 through 130 Processing helix chain 'L' and resid 185 through 189 Processing helix chain 'N' and resid 88 through 92 removed outlier: 3.974A pdb=" N THR N 92 " --> pdb=" O PRO N 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 118 removed outlier: 3.722A pdb=" N ASP R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 124 No H-bonds generated for 'chain 'R' and resid 122 through 124' Processing helix chain 'R' and resid 125 through 133 removed outlier: 4.044A pdb=" N GLN R 131 " --> pdb=" O LEU R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 165 removed outlier: 3.985A pdb=" N LEU R 142 " --> pdb=" O ARG R 138 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU R 143 " --> pdb=" O GLY R 139 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLN R 144 " --> pdb=" O ALA R 140 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE R 147 " --> pdb=" O LEU R 143 " (cutoff:3.500A) Proline residue: R 156 - end of helix removed outlier: 3.775A pdb=" N ASP R 163 " --> pdb=" O GLY R 159 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG R 164 " --> pdb=" O TYR R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 185 removed outlier: 3.809A pdb=" N ILE R 170 " --> pdb=" O ASN R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 188 No H-bonds generated for 'chain 'R' and resid 186 through 188' Processing helix chain 'R' and resid 193 through 222 removed outlier: 3.528A pdb=" N VAL R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR R 210 " --> pdb=" O GLY R 206 " (cutoff:3.500A) Proline residue: R 215 - end of helix removed outlier: 3.582A pdb=" N LEU R 221 " --> pdb=" O ILE R 217 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE R 222 " --> pdb=" O ILE R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 236 Processing helix chain 'R' and resid 237 through 257 removed outlier: 3.775A pdb=" N TYR R 246 " --> pdb=" O SER R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 264 removed outlier: 3.617A pdb=" N ARG R 264 " --> pdb=" O TRP R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 277 removed outlier: 4.159A pdb=" N LEU R 269 " --> pdb=" O VAL R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 310 removed outlier: 4.090A pdb=" N ALA R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE R 310 " --> pdb=" O MET R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 347 Proline residue: R 337 - end of helix Processing helix chain 'R' and resid 361 through 389 removed outlier: 3.912A pdb=" N PHE R 372 " --> pdb=" O ALA R 368 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE R 375 " --> pdb=" O CYS R 371 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL R 378 " --> pdb=" O GLY R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 394 through 412 removed outlier: 3.517A pdb=" N LEU R 398 " --> pdb=" O ARG R 394 " (cutoff:3.500A) Processing helix chain 'R' and resid 413 through 418 Processing helix chain 'R' and resid 422 through 437 removed outlier: 3.747A pdb=" N PHE R 437 " --> pdb=" O GLU R 433 " (cutoff:3.500A) Processing helix chain 'R' and resid 442 through 451 Processing helix chain 'R' and resid 455 through 471 removed outlier: 3.626A pdb=" N ALA R 461 " --> pdb=" O ALA R 457 " (cutoff:3.500A) Processing helix chain 'R' and resid 474 through 489 removed outlier: 3.629A pdb=" N LEU R 478 " --> pdb=" O GLY R 474 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER R 489 " --> pdb=" O LEU R 485 " (cutoff:3.500A) Processing helix chain 'R' and resid 493 through 505 removed outlier: 3.902A pdb=" N LEU R 501 " --> pdb=" O GLU R 497 " (cutoff:3.500A) Processing helix chain 'R' and resid 506 through 541 removed outlier: 3.890A pdb=" N PHE R 510 " --> pdb=" O MET R 506 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE R 525 " --> pdb=" O ALA R 521 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL R 527 " --> pdb=" O ALA R 523 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N SER R 528 " --> pdb=" O LEU R 524 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA R 541 " --> pdb=" O VAL R 537 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'H' and resid 7 through 11 Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 16 removed outlier: 6.255A pdb=" N GLY H 14 " --> pdb=" O THR H 129 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ARG H 42 " --> pdb=" O TRP H 51 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TRP H 51 " --> pdb=" O ARG H 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 139 through 143 removed outlier: 6.066A pdb=" N TYR H 195 " --> pdb=" O ASP H 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 150 through 151 removed outlier: 6.066A pdb=" N TYR H 195 " --> pdb=" O ASP H 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 170 through 173 removed outlier: 4.327A pdb=" N TYR H 213 " --> pdb=" O VAL H 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 7 through 9 Processing sheet with id=AA7, first strand: chain 'L' and resid 12 through 15 removed outlier: 3.536A pdb=" N ALA L 15 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 12 through 15 removed outlier: 3.536A pdb=" N ALA L 15 " --> pdb=" O GLU L 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.953A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 146 through 152 Processing sheet with id=AB2, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AB3, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.649A pdb=" N TRP N 37 " --> pdb=" O VAL N 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AB5, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.603A pdb=" N GLY K 10 " --> pdb=" O THR K 118 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.603A pdb=" N GLY K 10 " --> pdb=" O THR K 118 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR K 110 " --> pdb=" O ILE K 98 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1296 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: 1.31 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2652 1.34 - 1.47: 2343 1.47 - 1.60: 3581 1.60 - 1.73: 1 1.73 - 1.85: 60 Bond restraints: 8637 Sorted by residual: bond pdb=" O21 J89 R 601 " pdb=" P22 J89 R 601 " ideal model delta sigma weight residual 1.716 1.853 -0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" C17 J89 R 601 " pdb=" C20 J89 R 601 " ideal model delta sigma weight residual 1.536 1.672 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" N TYR H 104 " pdb=" CA TYR H 104 " ideal model delta sigma weight residual 1.458 1.490 -0.031 9.00e-03 1.23e+04 1.22e+01 bond pdb=" C20 J89 R 601 " pdb=" O21 J89 R 601 " ideal model delta sigma weight residual 1.390 1.333 0.057 2.00e-02 2.50e+03 8.25e+00 bond pdb=" N ASN H 116 " pdb=" CA ASN H 116 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.18e+00 ... (remaining 8632 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 11352 2.28 - 4.56: 316 4.56 - 6.83: 52 6.83 - 9.11: 12 9.11 - 11.39: 1 Bond angle restraints: 11733 Sorted by residual: angle pdb=" N GLY H 117 " pdb=" CA GLY H 117 " pdb=" C GLY H 117 " ideal model delta sigma weight residual 112.50 119.67 -7.17 1.16e+00 7.43e-01 3.82e+01 angle pdb=" N THR N 34 " pdb=" CA THR N 34 " pdb=" C THR N 34 " ideal model delta sigma weight residual 114.75 121.94 -7.19 1.26e+00 6.30e-01 3.25e+01 angle pdb=" N LEU N 35 " pdb=" CA LEU N 35 " pdb=" C LEU N 35 " ideal model delta sigma weight residual 109.06 117.45 -8.39 1.70e+00 3.46e-01 2.44e+01 angle pdb=" N TYR N 33 " pdb=" CA TYR N 33 " pdb=" C TYR N 33 " ideal model delta sigma weight residual 109.23 101.61 7.62 1.55e+00 4.16e-01 2.42e+01 angle pdb=" N ARG R 164 " pdb=" CA ARG R 164 " pdb=" C ARG R 164 " ideal model delta sigma weight residual 111.40 117.20 -5.80 1.22e+00 6.72e-01 2.26e+01 ... (remaining 11728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.76: 4882 25.76 - 51.52: 152 51.52 - 77.27: 23 77.27 - 103.03: 4 103.03 - 128.79: 2 Dihedral angle restraints: 5063 sinusoidal: 1900 harmonic: 3163 Sorted by residual: dihedral pdb=" CB CYS H 159 " pdb=" SG CYS H 159 " pdb=" SG CYS H 215 " pdb=" CB CYS H 215 " ideal model delta sinusoidal sigma weight residual 93.00 56.21 36.79 1 1.00e+01 1.00e-02 1.91e+01 dihedral pdb=" C16 J89 R 601 " pdb=" C17 J89 R 601 " pdb=" C18 J89 R 601 " pdb=" O19 J89 R 601 " ideal model delta sinusoidal sigma weight residual 307.51 178.72 128.79 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C THR N 34 " pdb=" N THR N 34 " pdb=" CA THR N 34 " pdb=" CB THR N 34 " ideal model delta harmonic sigma weight residual -122.00 -132.22 10.22 0 2.50e+00 1.60e-01 1.67e+01 ... (remaining 5060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1295 0.128 - 0.255: 20 0.255 - 0.383: 1 0.383 - 0.511: 1 0.511 - 0.638: 1 Chirality restraints: 1318 Sorted by residual: chirality pdb=" CG LEU N 35 " pdb=" CB LEU N 35 " pdb=" CD1 LEU N 35 " pdb=" CD2 LEU N 35 " both_signs ideal model delta sigma weight residual False -2.59 -1.95 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA THR N 34 " pdb=" N THR N 34 " pdb=" C THR N 34 " pdb=" CB THR N 34 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" CA HIS H 110 " pdb=" N HIS H 110 " pdb=" C HIS H 110 " pdb=" CB HIS H 110 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 1315 not shown) Planarity restraints: 1477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 178 " 0.043 2.00e-02 2.50e+03 2.18e-02 1.18e+01 pdb=" CG TRP R 178 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP R 178 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP R 178 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP R 178 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP R 178 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP R 178 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 178 " 0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 178 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 178 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR N 122 " -0.054 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO N 123 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO N 123 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO N 123 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 110 " 0.032 2.00e-02 2.50e+03 2.67e-02 1.07e+01 pdb=" CG HIS H 110 " -0.019 2.00e-02 2.50e+03 pdb=" ND1 HIS H 110 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 HIS H 110 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS H 110 " 0.023 2.00e-02 2.50e+03 pdb=" NE2 HIS H 110 " 0.023 2.00e-02 2.50e+03 ... (remaining 1474 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2551 2.82 - 3.34: 7020 3.34 - 3.86: 12859 3.86 - 4.38: 14257 4.38 - 4.90: 26780 Nonbonded interactions: 63467 Sorted by model distance: nonbonded pdb=" OG SER K 35 " pdb=" OH TYR K 108 " model vdw 2.303 3.040 nonbonded pdb=" OG1 THR N 34 " pdb=" NH2 ARG N 73 " model vdw 2.308 3.120 nonbonded pdb=" OG SER R 250 " pdb=" OG SER R 363 " model vdw 2.313 3.040 nonbonded pdb=" O CYS N 104 " pdb=" ND2 ASN R 538 " model vdw 2.360 3.120 nonbonded pdb=" O TRP H 115 " pdb=" OG SER L 52 " model vdw 2.402 3.040 ... (remaining 63462 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.360 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.350 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 0.137 8643 Z= 0.351 Angle : 0.928 11.389 11745 Z= 0.523 Chirality : 0.057 0.638 1318 Planarity : 0.006 0.083 1477 Dihedral : 13.618 128.789 3035 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.25), residues: 1091 helix: 0.66 (0.27), residues: 367 sheet: 0.33 (0.29), residues: 316 loop : -1.62 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 28 TYR 0.030 0.002 TYR N 33 PHE 0.056 0.003 PHE R 526 TRP 0.048 0.003 TRP R 178 HIS 0.017 0.002 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00805 / 0.35 ( 8637) covalent geometry : angle 0.92568 / 0.52 (11733) SS BOND : bond 0.01408 / 0.80 ( 6) SS BOND : angle 2.23338 / 1.23 ( 12) hydrogen bonds : bond 0.14353 / 9.33 ( 457) hydrogen bonds : angle 5.94385 / 4.05 ( 1296) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.308 Fit side-chains REVERT: H 77 ASP cc_start: 0.7586 (t70) cc_final: 0.7201 (t0) REVERT: R 258 ASP cc_start: 0.7548 (t0) cc_final: 0.7291 (t70) REVERT: R 500 SER cc_start: 0.8209 (m) cc_final: 0.7986 (m) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.5454 time to fit residues: 56.4134 Evaluate side-chains 80 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.0570 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN N 60 ASN R 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.198651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.149472 restraints weight = 9446.961| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.61 r_work: 0.3305 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8643 Z= 0.132 Angle : 0.595 7.389 11745 Z= 0.318 Chirality : 0.043 0.200 1318 Planarity : 0.005 0.055 1477 Dihedral : 8.070 130.745 1228 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.77 % Allowed : 6.71 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.26), residues: 1091 helix: 1.64 (0.29), residues: 366 sheet: 0.75 (0.30), residues: 313 loop : -1.31 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 28 TYR 0.018 0.001 TYR R 160 PHE 0.017 0.001 PHE R 526 TRP 0.027 0.001 TRP R 178 HIS 0.006 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 ( 8637) covalent geometry : angle 0.59377 / 0.32 (11733) SS BOND : bond 0.00718 / 0.39 ( 6) SS BOND : angle 1.28025 / 0.72 ( 12) hydrogen bonds : bond 0.05748 / 3.95 ( 457) hydrogen bonds : angle 4.63624 / 3.18 ( 1296) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.270 Fit side-chains REVERT: L 107 GLU cc_start: 0.7305 (pt0) cc_final: 0.7009 (pt0) REVERT: N 28 ARG cc_start: 0.7396 (mmt90) cc_final: 0.6998 (mmt-90) REVERT: N 44 LYS cc_start: 0.7736 (mttm) cc_final: 0.7501 (mttt) REVERT: N 108 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7333 (ttp) outliers start: 7 outliers final: 4 residues processed: 91 average time/residue: 0.5620 time to fit residues: 54.4929 Evaluate side-chains 81 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 108 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 76 optimal weight: 0.0770 chunk 102 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 overall best weight: 2.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN H 116 ASN H 190 GLN L 5 GLN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.191417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140246 restraints weight = 9358.340| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.95 r_work: 0.3141 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8643 Z= 0.236 Angle : 0.696 8.139 11745 Z= 0.376 Chirality : 0.047 0.238 1318 Planarity : 0.005 0.058 1477 Dihedral : 7.942 123.577 1228 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.98 % Allowed : 8.69 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.26), residues: 1091 helix: 1.41 (0.28), residues: 368 sheet: 0.87 (0.32), residues: 285 loop : -1.36 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 28 TYR 0.031 0.002 TYR N 33 PHE 0.026 0.002 PHE R 526 TRP 0.030 0.002 TRP R 178 HIS 0.011 0.002 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.24 ( 8637) covalent geometry : angle 0.69413 / 0.38 (11733) SS BOND : bond 0.01210 / 0.69 ( 6) SS BOND : angle 1.84555 / 1.04 ( 12) hydrogen bonds : bond 0.08049 / 5.50 ( 457) hydrogen bonds : angle 4.76935 / 3.28 ( 1296) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.333 Fit side-chains REVERT: N 28 ARG cc_start: 0.7427 (mmt90) cc_final: 0.7020 (mmt-90) REVERT: R 179 SER cc_start: 0.8147 (m) cc_final: 0.7945 (m) REVERT: R 254 GLN cc_start: 0.7948 (tp40) cc_final: 0.7534 (tm-30) REVERT: R 538 ASN cc_start: 0.7864 (m-40) cc_final: 0.7625 (m-40) outliers start: 18 outliers final: 10 residues processed: 95 average time/residue: 0.5407 time to fit residues: 54.9407 Evaluate side-chains 90 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 307 LYS Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 68 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 0.0020 chunk 105 optimal weight: 40.0000 chunk 91 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN L 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.196993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148171 restraints weight = 9508.031| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 4.17 r_work: 0.3256 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8643 Z= 0.130 Angle : 0.559 6.973 11745 Z= 0.301 Chirality : 0.043 0.197 1318 Planarity : 0.004 0.056 1477 Dihedral : 7.538 124.291 1228 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.65 % Allowed : 10.34 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.27), residues: 1091 helix: 1.94 (0.29), residues: 360 sheet: 0.89 (0.30), residues: 309 loop : -1.16 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 164 TYR 0.021 0.001 TYR R 160 PHE 0.012 0.001 PHE R 526 TRP 0.027 0.001 TRP R 178 HIS 0.007 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 ( 8637) covalent geometry : angle 0.55792 / 0.30 (11733) SS BOND : bond 0.00737 / 0.41 ( 6) SS BOND : angle 1.23679 / 0.70 ( 12) hydrogen bonds : bond 0.05602 / 3.86 ( 457) hydrogen bonds : angle 4.39114 / 3.02 ( 1296) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.249 Fit side-chains REVERT: H 54 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.7887 (t80) REVERT: H 180 SER cc_start: 0.6589 (t) cc_final: 0.6303 (m) REVERT: L 201 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7335 (tp40) REVERT: N 28 ARG cc_start: 0.7291 (mmt90) cc_final: 0.6917 (mmt-90) REVERT: N 108 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6960 (ttp) REVERT: R 179 SER cc_start: 0.7927 (m) cc_final: 0.7721 (m) REVERT: R 254 GLN cc_start: 0.7855 (tp40) cc_final: 0.7546 (tm-30) REVERT: R 500 SER cc_start: 0.8223 (m) cc_final: 0.7941 (m) REVERT: R 534 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7225 (mt-10) REVERT: R 538 ASN cc_start: 0.7389 (m-40) cc_final: 0.7183 (m-40) outliers start: 15 outliers final: 7 residues processed: 100 average time/residue: 0.5130 time to fit residues: 54.8003 Evaluate side-chains 94 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain L residue 201 GLN Chi-restraints excluded: chain N residue 108 MET Chi-restraints excluded: chain R residue 307 LYS Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 77 optimal weight: 0.0470 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN L 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.196383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.145197 restraints weight = 9435.771| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 3.97 r_work: 0.3222 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8643 Z= 0.140 Angle : 0.569 6.508 11745 Z= 0.304 Chirality : 0.043 0.168 1318 Planarity : 0.004 0.055 1477 Dihedral : 7.314 122.123 1228 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.98 % Allowed : 11.77 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.27), residues: 1091 helix: 1.99 (0.28), residues: 360 sheet: 0.91 (0.30), residues: 312 loop : -1.07 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 164 TYR 0.021 0.001 TYR R 160 PHE 0.013 0.001 PHE R 526 TRP 0.022 0.001 TRP R 178 HIS 0.007 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 8637) covalent geometry : angle 0.56792 / 0.30 (11733) SS BOND : bond 0.00817 / 0.46 ( 6) SS BOND : angle 1.31026 / 0.74 ( 12) hydrogen bonds : bond 0.05747 / 3.96 ( 457) hydrogen bonds : angle 4.32332 / 2.97 ( 1296) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.302 Fit side-chains REVERT: H 54 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.7920 (t80) REVERT: H 180 SER cc_start: 0.6586 (t) cc_final: 0.6297 (m) REVERT: N 28 ARG cc_start: 0.7314 (mmt90) cc_final: 0.6950 (mmt-90) REVERT: N 108 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6955 (ttp) REVERT: R 179 SER cc_start: 0.7875 (m) cc_final: 0.7668 (m) REVERT: R 254 GLN cc_start: 0.7831 (tp40) cc_final: 0.7586 (tm-30) REVERT: R 500 SER cc_start: 0.8228 (m) cc_final: 0.7944 (m) REVERT: R 534 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7261 (mt-10) REVERT: K 34 MET cc_start: 0.6411 (ptm) cc_final: 0.6039 (ptt) outliers start: 18 outliers final: 10 residues processed: 100 average time/residue: 0.5497 time to fit residues: 58.6326 Evaluate side-chains 100 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 108 MET Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 307 LYS Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain K residue 35 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 44 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 14 optimal weight: 0.5980 chunk 105 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.194513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.143878 restraints weight = 9360.474| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 3.59 r_work: 0.3199 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8643 Z= 0.171 Angle : 0.611 9.244 11745 Z= 0.327 Chirality : 0.044 0.269 1318 Planarity : 0.005 0.053 1477 Dihedral : 7.260 120.970 1228 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.20 % Allowed : 11.77 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.26), residues: 1091 helix: 1.91 (0.28), residues: 360 sheet: 1.08 (0.32), residues: 288 loop : -1.05 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 164 TYR 0.022 0.002 TYR R 160 PHE 0.014 0.001 PHE R 151 TRP 0.026 0.002 TRP R 178 HIS 0.008 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 8637) covalent geometry : angle 0.60971 / 0.33 (11733) SS BOND : bond 0.00923 / 0.51 ( 6) SS BOND : angle 1.48751 / 0.84 ( 12) hydrogen bonds : bond 0.06510 / 4.48 ( 457) hydrogen bonds : angle 4.38963 / 3.01 ( 1296) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.307 Fit side-chains REVERT: H 47 LYS cc_start: 0.8302 (mtmt) cc_final: 0.8043 (mtpt) REVERT: H 54 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.7928 (t80) REVERT: H 180 SER cc_start: 0.6595 (t) cc_final: 0.6302 (m) REVERT: N 28 ARG cc_start: 0.7391 (mmt90) cc_final: 0.7022 (mmt-90) REVERT: N 108 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7157 (ttp) REVERT: R 179 SER cc_start: 0.7968 (m) cc_final: 0.7760 (m) REVERT: R 334 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7283 (tpt) REVERT: R 500 SER cc_start: 0.8283 (m) cc_final: 0.7994 (m) REVERT: K 20 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6985 (tt) REVERT: K 34 MET cc_start: 0.6626 (ptm) cc_final: 0.6411 (ptt) outliers start: 20 outliers final: 14 residues processed: 98 average time/residue: 0.5218 time to fit residues: 54.8665 Evaluate side-chains 102 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain N residue 33 TYR Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 108 MET Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 271 MET Chi-restraints excluded: chain R residue 307 LYS Chi-restraints excluded: chain R residue 334 MET Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 23 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.192428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.140537 restraints weight = 9490.014| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 4.08 r_work: 0.3137 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8643 Z= 0.215 Angle : 0.661 7.547 11745 Z= 0.355 Chirality : 0.046 0.253 1318 Planarity : 0.005 0.052 1477 Dihedral : 7.404 121.261 1228 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.09 % Allowed : 13.64 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.26), residues: 1091 helix: 1.72 (0.28), residues: 362 sheet: 1.02 (0.32), residues: 286 loop : -1.20 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 164 TYR 0.023 0.002 TYR R 160 PHE 0.017 0.002 PHE R 151 TRP 0.027 0.002 TRP R 178 HIS 0.009 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.21 ( 8637) covalent geometry : angle 0.65900 / 0.35 (11733) SS BOND : bond 0.01089 / 0.61 ( 6) SS BOND : angle 1.71649 / 0.97 ( 12) hydrogen bonds : bond 0.07514 / 5.15 ( 457) hydrogen bonds : angle 4.55416 / 3.13 ( 1296) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.374 Fit side-chains REVERT: H 47 LYS cc_start: 0.8274 (mtmt) cc_final: 0.7966 (mtpt) REVERT: H 54 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.7982 (t80) REVERT: L 6 MET cc_start: 0.8492 (mtm) cc_final: 0.7305 (mtm) REVERT: N 28 ARG cc_start: 0.7357 (mmt90) cc_final: 0.7017 (mmt-90) REVERT: R 179 SER cc_start: 0.7918 (m) cc_final: 0.7704 (m) REVERT: R 254 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7732 (tm-30) REVERT: R 500 SER cc_start: 0.8272 (m) cc_final: 0.7954 (m) REVERT: K 34 MET cc_start: 0.6730 (ptm) cc_final: 0.6401 (ptt) outliers start: 19 outliers final: 11 residues processed: 97 average time/residue: 0.5220 time to fit residues: 54.2755 Evaluate side-chains 101 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain N residue 33 TYR Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 152 MET Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 0.7980 chunk 6 optimal weight: 0.0570 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.195212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.143082 restraints weight = 9376.269| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 4.11 r_work: 0.3193 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8643 Z= 0.157 Angle : 0.594 7.355 11745 Z= 0.318 Chirality : 0.043 0.163 1318 Planarity : 0.004 0.054 1477 Dihedral : 7.310 121.533 1228 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.21 % Allowed : 14.96 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.26), residues: 1091 helix: 1.97 (0.28), residues: 359 sheet: 1.04 (0.32), residues: 288 loop : -1.05 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 73 TYR 0.023 0.001 TYR R 160 PHE 0.013 0.001 PHE R 151 TRP 0.027 0.002 TRP R 178 HIS 0.007 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 8637) covalent geometry : angle 0.59217 / 0.32 (11733) SS BOND : bond 0.00856 / 0.47 ( 6) SS BOND : angle 1.45007 / 0.82 ( 12) hydrogen bonds : bond 0.06253 / 4.31 ( 457) hydrogen bonds : angle 4.38340 / 3.01 ( 1296) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.288 Fit side-chains REVERT: H 47 LYS cc_start: 0.8263 (mtmt) cc_final: 0.8009 (mtpt) REVERT: H 54 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.7971 (t80) REVERT: H 180 SER cc_start: 0.6571 (t) cc_final: 0.6285 (m) REVERT: L 6 MET cc_start: 0.8489 (mtm) cc_final: 0.7344 (mtm) REVERT: N 28 ARG cc_start: 0.7199 (mmt90) cc_final: 0.6907 (mmt-90) REVERT: R 179 SER cc_start: 0.7853 (m) cc_final: 0.7649 (m) REVERT: R 254 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7694 (tm-30) REVERT: R 334 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7176 (tpt) REVERT: R 500 SER cc_start: 0.8248 (m) cc_final: 0.7926 (m) REVERT: K 34 MET cc_start: 0.6761 (ptm) cc_final: 0.6385 (ptt) outliers start: 11 outliers final: 9 residues processed: 99 average time/residue: 0.5090 time to fit residues: 54.0108 Evaluate side-chains 97 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 218 ILE Chi-restraints excluded: chain R residue 334 MET Chi-restraints excluded: chain R residue 409 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.196728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146797 restraints weight = 9391.438| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 3.60 r_work: 0.3237 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8643 Z= 0.139 Angle : 0.580 11.061 11745 Z= 0.307 Chirality : 0.043 0.262 1318 Planarity : 0.004 0.056 1477 Dihedral : 7.156 119.565 1228 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.21 % Allowed : 14.96 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.27), residues: 1091 helix: 2.13 (0.29), residues: 359 sheet: 0.87 (0.30), residues: 314 loop : -0.96 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 164 TYR 0.023 0.001 TYR R 160 PHE 0.013 0.001 PHE R 151 TRP 0.027 0.001 TRP R 178 HIS 0.007 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 8637) covalent geometry : angle 0.57883 / 0.31 (11733) SS BOND : bond 0.00794 / 0.44 ( 6) SS BOND : angle 1.32956 / 0.75 ( 12) hydrogen bonds : bond 0.05667 / 3.91 ( 457) hydrogen bonds : angle 4.27611 / 2.94 ( 1296) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.314 Fit side-chains REVERT: H 47 LYS cc_start: 0.8336 (mtmt) cc_final: 0.8081 (mtpt) REVERT: H 54 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.7965 (t80) REVERT: H 180 SER cc_start: 0.6675 (t) cc_final: 0.6378 (m) REVERT: L 6 MET cc_start: 0.8532 (mtm) cc_final: 0.7503 (mtm) REVERT: N 28 ARG cc_start: 0.7269 (mmt90) cc_final: 0.6983 (mmt-90) REVERT: R 254 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7725 (tm-30) REVERT: R 500 SER cc_start: 0.8280 (m) cc_final: 0.7989 (m) REVERT: R 534 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7349 (mt-10) REVERT: K 34 MET cc_start: 0.6787 (ptm) cc_final: 0.6408 (ptt) outliers start: 11 outliers final: 9 residues processed: 102 average time/residue: 0.5128 time to fit residues: 56.1104 Evaluate side-chains 100 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.194077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.144068 restraints weight = 9388.207| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 4.12 r_work: 0.3185 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8643 Z= 0.183 Angle : 0.628 9.882 11745 Z= 0.335 Chirality : 0.045 0.265 1318 Planarity : 0.005 0.055 1477 Dihedral : 7.264 119.563 1228 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.21 % Allowed : 15.51 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.26), residues: 1091 helix: 1.98 (0.28), residues: 359 sheet: 1.04 (0.32), residues: 289 loop : -0.99 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 164 TYR 0.023 0.002 TYR R 160 PHE 0.015 0.001 PHE R 151 TRP 0.027 0.002 TRP R 178 HIS 0.008 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 8637) covalent geometry : angle 0.62675 / 0.33 (11733) SS BOND : bond 0.00971 / 0.54 ( 6) SS BOND : angle 1.58749 / 0.90 ( 12) hydrogen bonds : bond 0.06693 / 4.60 ( 457) hydrogen bonds : angle 4.39659 / 3.03 ( 1296) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.313 Fit side-chains REVERT: H 47 LYS cc_start: 0.8318 (mtmt) cc_final: 0.8069 (mtpt) REVERT: H 54 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.7969 (t80) REVERT: H 110 HIS cc_start: 0.8528 (OUTLIER) cc_final: 0.8058 (p90) REVERT: H 180 SER cc_start: 0.6692 (t) cc_final: 0.6423 (m) REVERT: L 6 MET cc_start: 0.8507 (mtm) cc_final: 0.7362 (mtm) REVERT: N 28 ARG cc_start: 0.7300 (mmt90) cc_final: 0.6991 (mmt-90) REVERT: R 254 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7754 (tm-30) REVERT: R 500 SER cc_start: 0.8284 (m) cc_final: 0.7964 (m) REVERT: K 34 MET cc_start: 0.6663 (ptm) cc_final: 0.6271 (ptt) outliers start: 11 outliers final: 10 residues processed: 93 average time/residue: 0.5608 time to fit residues: 55.6965 Evaluate side-chains 96 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 157 LEU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 13 optimal weight: 0.0370 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 68 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 ASN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 132 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.199312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.149387 restraints weight = 9361.514| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 3.41 r_work: 0.3284 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8643 Z= 0.118 Angle : 0.544 9.749 11745 Z= 0.287 Chirality : 0.042 0.240 1318 Planarity : 0.004 0.056 1477 Dihedral : 6.956 118.649 1228 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.99 % Allowed : 15.51 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.27), residues: 1091 helix: 2.25 (0.29), residues: 360 sheet: 0.90 (0.30), residues: 315 loop : -0.89 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 164 TYR 0.027 0.001 TYR R 160 PHE 0.013 0.001 PHE R 151 TRP 0.027 0.001 TRP R 178 HIS 0.005 0.001 HIS H 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 ( 8637) covalent geometry : angle 0.54281 / 0.29 (11733) SS BOND : bond 0.00632 / 0.34 ( 6) SS BOND : angle 1.16133 / 0.66 ( 12) hydrogen bonds : bond 0.04819 / 3.33 ( 457) hydrogen bonds : angle 4.12715 / 2.85 ( 1296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2760.87 seconds wall clock time: 47 minutes 47.67 seconds (2867.67 seconds total)