Starting phenix.real_space_refine on Tue Aug 4 22:20:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1n_36796/08_2026/8k1n_36796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1n_36796/08_2026/8k1n_36796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k1n_36796/08_2026/8k1n_36796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1n_36796/08_2026/8k1n_36796.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1n_36796/08_2026/8k1n_36796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1n_36796/08_2026/8k1n_36796.cif" } resolution = 3.0 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= -0.001 sd= 0.070 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 2 5.49 5 S 23 5.16 5 C 4591 2.51 5 N 1255 2.21 5 O 1304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7175 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 3858 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 20, 'TRANS': 509} Chain: "E" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1589 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 8, 'TRANS': 202} Chain: "D" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1589 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 8, 'TRANS': 202} Chain: "C" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 139 Unusual residues: {'CDL': 1, 'RFP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'RFP:plan-4': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.84, per 1000 atoms: 0.26 Number of scatterers: 7175 At special positions: 0 Unit cell: (68.224, 84.864, 109.824, 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 23 16.00 P 2 15.00 O 1304 8.00 N 1255 7.00 C 4591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.67 Conformation dependent library (CDL) restraints added in 413.0 milliseconds 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 56.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 78 through 82 removed outlier: 4.491A pdb=" N ARG D 82 " --> pdb=" O VAL D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 78 through 82' Processing helix chain 'D' and resid 99 through 109 removed outlier: 3.501A pdb=" N MET D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 125 removed outlier: 3.620A pdb=" N GLU D 120 " --> pdb=" O ALA D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 150 removed outlier: 3.671A pdb=" N GLN D 142 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS D 143 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL D 144 " --> pdb=" O ASN D 140 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 183 removed outlier: 3.909A pdb=" N GLN D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 201 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 40 through 63 removed outlier: 3.686A pdb=" N LEU C 48 " --> pdb=" O TRP C 44 " (cutoff:3.500A) Proline residue: C 51 - end of helix removed outlier: 3.751A pdb=" N THR C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ALA C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 79 Processing helix chain 'C' and resid 81 through 87 Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 101 through 125 removed outlier: 5.365A pdb=" N MET C 105 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N PHE C 106 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N HIS C 107 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALA C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ASP C 125 " --> pdb=" O HIS C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 removed outlier: 4.603A pdb=" N ASP C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 169 removed outlier: 3.593A pdb=" N ALA C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 200 removed outlier: 3.534A pdb=" N VAL C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 228 Processing helix chain 'C' and resid 232 through 236 removed outlier: 4.274A pdb=" N CYS C 236 " --> pdb=" O THR C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 232 through 236' Processing helix chain 'C' and resid 238 through 244 removed outlier: 3.776A pdb=" N SER C 242 " --> pdb=" O PRO C 238 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 275 removed outlier: 4.143A pdb=" N LEU C 257 " --> pdb=" O TRP C 253 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU C 258 " --> pdb=" O TRP C 254 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 306 Processing helix chain 'C' and resid 309 through 329 removed outlier: 4.010A pdb=" N SER C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 336 removed outlier: 7.416A pdb=" N ASP C 335 " --> pdb=" O HIS C 331 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLN C 336 " --> pdb=" O GLY C 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 331 through 336' Processing helix chain 'C' and resid 344 through 350 removed outlier: 4.844A pdb=" N THR C 348 " --> pdb=" O ARG C 344 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG C 349 " --> pdb=" O ASP C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 388 removed outlier: 3.706A pdb=" N PHE C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 362 " --> pdb=" O GLN C 358 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N MET C 370 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU C 383 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS C 384 " --> pdb=" O THR C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 397 Processing helix chain 'C' and resid 405 through 436 removed outlier: 6.820A pdb=" N HIS C 409 " --> pdb=" O TRP C 405 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 467 removed outlier: 3.910A pdb=" N GLN C 453 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) Proline residue: C 455 - end of helix removed outlier: 3.574A pdb=" N LEU C 459 " --> pdb=" O PRO C 455 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LEU C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER C 461 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL C 463 " --> pdb=" O LEU C 459 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 493 Proline residue: C 476 - end of helix removed outlier: 5.026A pdb=" N TRP C 479 " --> pdb=" O THR C 475 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY C 480 " --> pdb=" O PRO C 476 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER C 493 " --> pdb=" O TYR C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 503 removed outlier: 5.278A pdb=" N ASN C 503 " --> pdb=" O GLN C 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 499 through 503' Processing helix chain 'C' and resid 507 through 510 No H-bonds generated for 'chain 'C' and resid 507 through 510' Processing helix chain 'C' and resid 522 through 540 Processing helix chain 'E' and resid 48 through 55 Processing helix chain 'E' and resid 78 through 82 removed outlier: 4.480A pdb=" N ARG E 82 " --> pdb=" O VAL E 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 78 through 82' Processing helix chain 'E' and resid 99 through 109 removed outlier: 3.511A pdb=" N LEU E 106 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA E 107 " --> pdb=" O ILE E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 125 removed outlier: 3.621A pdb=" N GLU E 120 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 150 removed outlier: 3.680A pdb=" N LYS E 143 " --> pdb=" O GLY E 139 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL E 144 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER E 145 " --> pdb=" O ARG E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 183 removed outlier: 3.910A pdb=" N GLN E 183 " --> pdb=" O GLY E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 201 304 hydrogen bonds defined for protein. 912 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: 0.96 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1143 1.28 - 1.41: 1704 1.41 - 1.54: 4375 1.54 - 1.67: 42 1.67 - 1.81: 39 Bond restraints: 7303 Sorted by residual: bond pdb=" C ARG E 53 " pdb=" O ARG E 53 " ideal model delta sigma weight residual 1.236 1.144 0.092 1.32e-02 5.74e+03 4.85e+01 bond pdb=" C ALA E 107 " pdb=" O ALA E 107 " ideal model delta sigma weight residual 1.236 1.159 0.078 1.25e-02 6.40e+03 3.85e+01 bond pdb=" C ARG D 53 " pdb=" O ARG D 53 " ideal model delta sigma weight residual 1.236 1.156 0.080 1.32e-02 5.74e+03 3.65e+01 bond pdb=" CA ALA D 107 " pdb=" CB ALA D 107 " ideal model delta sigma weight residual 1.532 1.450 0.083 1.53e-02 4.27e+03 2.93e+01 bond pdb=" CA ALA D 154 " pdb=" CB ALA D 154 " ideal model delta sigma weight residual 1.529 1.447 0.082 1.54e-02 4.22e+03 2.85e+01 ... (remaining 7298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 9300 2.36 - 4.72: 480 4.72 - 7.09: 103 7.09 - 9.45: 29 9.45 - 11.81: 9 Bond angle restraints: 9921 Sorted by residual: angle pdb=" N ARG D 110 " pdb=" CA ARG D 110 " pdb=" C ARG D 110 " ideal model delta sigma weight residual 113.23 102.03 11.20 1.24e+00 6.50e-01 8.16e+01 angle pdb=" C ILE E 113 " pdb=" N ASP E 114 " pdb=" CA ASP E 114 " ideal model delta sigma weight residual 122.42 132.66 -10.24 1.33e+00 5.65e-01 5.92e+01 angle pdb=" N ILE C 346 " pdb=" CA ILE C 346 " pdb=" C ILE C 346 " ideal model delta sigma weight residual 111.56 105.21 6.35 8.60e-01 1.35e+00 5.45e+01 angle pdb=" N VAL E 22 " pdb=" CA VAL E 22 " pdb=" C VAL E 22 " ideal model delta sigma weight residual 112.90 105.83 7.07 9.60e-01 1.09e+00 5.42e+01 angle pdb=" C LYS E 131 " pdb=" N LYS E 132 " pdb=" CA LYS E 132 " ideal model delta sigma weight residual 120.94 109.62 11.32 1.57e+00 4.06e-01 5.20e+01 ... (remaining 9916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 3850 17.25 - 34.50: 382 34.50 - 51.75: 89 51.75 - 69.00: 39 69.00 - 86.25: 6 Dihedral angle restraints: 4366 sinusoidal: 1722 harmonic: 2644 Sorted by residual: dihedral pdb=" C PRO D 43 " pdb=" N PRO D 43 " pdb=" CA PRO D 43 " pdb=" CB PRO D 43 " ideal model delta harmonic sigma weight residual -120.70 -106.66 -14.04 0 2.50e+00 1.60e-01 3.16e+01 dihedral pdb=" CA GLY C 282 " pdb=" C GLY C 282 " pdb=" N LEU C 283 " pdb=" CA LEU C 283 " ideal model delta harmonic sigma weight residual 180.00 152.23 27.77 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" C VAL D 22 " pdb=" N VAL D 22 " pdb=" CA VAL D 22 " pdb=" CB VAL D 22 " ideal model delta harmonic sigma weight residual -122.00 -135.83 13.83 0 2.50e+00 1.60e-01 3.06e+01 ... (remaining 4363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1028 0.092 - 0.183: 126 0.183 - 0.275: 20 0.275 - 0.367: 6 0.367 - 0.458: 2 Chirality restraints: 1182 Sorted by residual: chirality pdb=" CB VAL E 91 " pdb=" CA VAL E 91 " pdb=" CG1 VAL E 91 " pdb=" CG2 VAL E 91 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA GLU D 203 " pdb=" N GLU D 203 " pdb=" C GLU D 203 " pdb=" CB GLU D 203 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA VAL D 22 " pdb=" N VAL D 22 " pdb=" C VAL D 22 " pdb=" CB VAL D 22 " both_signs ideal model delta sigma weight residual False 2.44 2.08 0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 1179 not shown) Planarity restraints: 1245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 RFP C 601 " 0.111 2.00e-02 2.50e+03 2.52e-01 6.33e+02 pdb=" C18 RFP C 601 " -0.344 2.00e-02 2.50e+03 pdb=" C19 RFP C 601 " 0.335 2.00e-02 2.50e+03 pdb=" C20 RFP C 601 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 RFP C 601 " -0.014 2.00e-02 2.50e+03 2.18e-01 5.96e+02 pdb=" C16 RFP C 601 " 0.085 2.00e-02 2.50e+03 pdb=" C17 RFP C 601 " 0.364 2.00e-02 2.50e+03 pdb=" C18 RFP C 601 " -0.264 2.00e-02 2.50e+03 pdb=" C30 RFP C 601 " -0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C15 RFP C 601 " 0.044 2.00e-02 2.50e+03 2.15e-01 5.79e+02 pdb=" C16 RFP C 601 " -0.057 2.00e-02 2.50e+03 pdb=" C2 RFP C 601 " -0.244 2.00e-02 2.50e+03 pdb=" N1 RFP C 601 " 0.387 2.00e-02 2.50e+03 pdb=" O11 RFP C 601 " -0.129 2.00e-02 2.50e+03 ... (remaining 1242 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1104 2.75 - 3.29: 6921 3.29 - 3.83: 11553 3.83 - 4.36: 14489 4.36 - 4.90: 24846 Nonbonded interactions: 58913 Sorted by model distance: nonbonded pdb=" O ILE C 134 " pdb=" OG1 THR C 137 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR C 33 " pdb=" OD1 ASN C 144 " model vdw 2.219 3.040 nonbonded pdb=" O PRO C 472 " pdb=" OG1 THR C 475 " model vdw 2.300 3.040 nonbonded pdb=" OG1 THR C 146 " pdb=" OH TYR C 271 " model vdw 2.336 3.040 nonbonded pdb=" OG SER E 192 " pdb=" OE2 GLU E 197 " model vdw 2.345 3.040 ... (remaining 58908 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 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } 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: 5.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.410 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:9.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 0.092 7303 Z= 0.535 Angle : 1.246 11.812 9921 Z= 0.806 Chirality : 0.066 0.458 1182 Planarity : 0.015 0.252 1245 Dihedral : 15.468 86.254 2686 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.70 % Allowed : 1.95 % Favored : 97.36 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % 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: -1.83 (0.26), residues: 946 helix: -0.23 (0.22), residues: 524 sheet: -1.56 (0.75), residues: 56 loop : -2.61 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 544 TYR 0.026 0.002 TYR C 56 PHE 0.027 0.003 PHE E 19 TRP 0.017 0.001 TRP C 44 HIS 0.011 0.002 HIS E 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.53 ( 7303) covalent geometry : angle 1.24613 / 0.81 ( 9921) hydrogen bonds : bond 0.14881 / 10.25 ( 304) hydrogen bonds : angle 6.19566 / 4.66 ( 912) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 0.218 Fit side-chains REVERT: C 78 MET cc_start: 0.7808 (mmm) cc_final: 0.7594 (mmm) REVERT: C 93 ASP cc_start: 0.7902 (p0) cc_final: 0.7307 (p0) REVERT: C 135 ASP cc_start: 0.6707 (t0) cc_final: 0.6454 (t70) REVERT: C 473 ARG cc_start: 0.7541 (ptt-90) cc_final: 0.7151 (pmt-80) REVERT: E 161 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7250 (mm-30) REVERT: D 123 GLU cc_start: 0.7351 (tt0) cc_final: 0.6555 (mm-30) REVERT: D 128 ASP cc_start: 0.7309 (t0) cc_final: 0.6915 (t70) REVERT: D 131 LYS cc_start: 0.8071 (mtmt) cc_final: 0.7434 (mmtt) REVERT: D 171 GLU cc_start: 0.7887 (tp30) cc_final: 0.7198 (mt-10) REVERT: D 204 LYS cc_start: 0.6686 (mttp) cc_final: 0.5544 (tmtt) REVERT: D 209 ARG cc_start: 0.6572 (ttm170) cc_final: 0.6106 (tpm170) outliers start: 5 outliers final: 0 residues processed: 149 average time/residue: 0.5400 time to fit residues: 84.3349 Evaluate side-chains 95 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 244 GLN E 193 HIS D 38 HIS D 193 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.142285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.118217 restraints weight = 8634.430| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.03 r_work: 0.3251 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7303 Z= 0.147 Angle : 0.718 19.553 9921 Z= 0.340 Chirality : 0.044 0.201 1182 Planarity : 0.005 0.068 1245 Dihedral : 13.236 124.628 1183 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.89 % Allowed : 10.99 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.20 (0.27), residues: 946 helix: 0.24 (0.23), residues: 542 sheet: -1.09 (0.74), residues: 58 loop : -2.41 (0.29), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 123 TYR 0.006 0.001 TYR C 56 PHE 0.021 0.002 PHE C 365 TRP 0.019 0.001 TRP C 44 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 7303) covalent geometry : angle 0.71794 / 0.34 ( 9921) hydrogen bonds : bond 0.03496 / 2.36 ( 304) hydrogen bonds : angle 3.84249 / 2.83 ( 912) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.249 Fit side-chains REVERT: C 93 ASP cc_start: 0.8285 (p0) cc_final: 0.7627 (p0) REVERT: C 125 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7447 (t70) REVERT: C 387 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: C 488 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7906 (tp) REVERT: E 161 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7662 (mm-30) REVERT: E 204 LYS cc_start: 0.7754 (mttp) cc_final: 0.7509 (ttmm) REVERT: D 128 ASP cc_start: 0.8010 (t0) cc_final: 0.7644 (t70) REVERT: D 131 LYS cc_start: 0.8643 (mtmt) cc_final: 0.7866 (mmtt) REVERT: D 171 GLU cc_start: 0.8426 (tp30) cc_final: 0.7794 (tt0) REVERT: D 209 ARG cc_start: 0.7252 (ttm170) cc_final: 0.6275 (tpm170) outliers start: 28 outliers final: 9 residues processed: 116 average time/residue: 0.5409 time to fit residues: 65.7395 Evaluate side-chains 113 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 34 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 67 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 86 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 48 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 68.8899 > 50:) chunk 12 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.139885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.115602 restraints weight = 8560.698| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.00 r_work: 0.3215 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 7303 Z= 0.134 Angle : 0.652 14.709 9921 Z= 0.307 Chirality : 0.042 0.157 1182 Planarity : 0.005 0.058 1245 Dihedral : 12.100 106.437 1183 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.59 % Allowed : 14.46 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.27), residues: 946 helix: 0.49 (0.23), residues: 542 sheet: -0.26 (1.22), residues: 24 loop : -2.22 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 344 TYR 0.003 0.001 TYR C 56 PHE 0.016 0.001 PHE C 191 TRP 0.017 0.001 TRP C 44 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 ( 7303) covalent geometry : angle 0.65179 / 0.31 ( 9921) hydrogen bonds : bond 0.03208 / 2.18 ( 304) hydrogen bonds : angle 3.59127 / 2.64 ( 912) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.196 Fit side-chains REVERT: C 93 ASP cc_start: 0.8289 (p0) cc_final: 0.7649 (p0) REVERT: C 296 MET cc_start: 0.8339 (mmm) cc_final: 0.8111 (mtp) REVERT: C 344 ARG cc_start: 0.8736 (mmm160) cc_final: 0.8519 (mmm160) REVERT: C 488 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7862 (tp) REVERT: E 161 GLU cc_start: 0.8549 (mt-10) cc_final: 0.7844 (mm-30) REVERT: E 206 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8453 (t) REVERT: D 131 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8061 (mmtt) REVERT: D 171 GLU cc_start: 0.8482 (tp30) cc_final: 0.7874 (tt0) REVERT: D 183 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7442 (mt0) outliers start: 33 outliers final: 10 residues processed: 119 average time/residue: 0.5320 time to fit residues: 66.3785 Evaluate side-chains 103 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 183 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 59 optimal weight: 0.0370 chunk 12 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 409 HIS E 38 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.113555 restraints weight = 8611.321| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.99 r_work: 0.3208 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 7303 Z= 0.135 Angle : 0.619 15.471 9921 Z= 0.295 Chirality : 0.042 0.147 1182 Planarity : 0.005 0.057 1245 Dihedral : 11.300 86.908 1183 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.45 % Allowed : 16.41 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.67 (0.27), residues: 946 helix: 0.67 (0.23), residues: 545 sheet: -1.01 (0.95), residues: 34 loop : -2.14 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 344 TYR 0.004 0.001 TYR C 322 PHE 0.015 0.001 PHE C 191 TRP 0.017 0.001 TRP C 44 HIS 0.003 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.13 ( 7303) covalent geometry : angle 0.61866 / 0.29 ( 9921) hydrogen bonds : bond 0.03029 / 2.07 ( 304) hydrogen bonds : angle 3.50603 / 2.59 ( 912) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.254 Fit side-chains REVERT: C 67 ARG cc_start: 0.7377 (ttt90) cc_final: 0.7123 (ttt90) REVERT: C 93 ASP cc_start: 0.8232 (p0) cc_final: 0.7555 (p0) REVERT: C 125 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7620 (t70) REVERT: C 344 ARG cc_start: 0.8780 (mmm160) cc_final: 0.8462 (mmm160) REVERT: C 387 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: C 473 ARG cc_start: 0.7884 (ptt-90) cc_final: 0.7324 (ptt-90) REVERT: C 488 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8201 (tt) REVERT: E 161 GLU cc_start: 0.8496 (mt-10) cc_final: 0.7862 (mm-30) REVERT: E 206 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8574 (t) REVERT: D 131 LYS cc_start: 0.8912 (mtmt) cc_final: 0.8130 (mmtt) REVERT: D 171 GLU cc_start: 0.8529 (tp30) cc_final: 0.7938 (tt0) REVERT: D 183 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7569 (mt0) outliers start: 32 outliers final: 12 residues processed: 115 average time/residue: 0.4720 time to fit residues: 57.1569 Evaluate side-chains 104 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 216 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 55 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 0.0070 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 193 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.138550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114263 restraints weight = 8550.222| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.99 r_work: 0.3199 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 7303 Z= 0.120 Angle : 0.594 15.356 9921 Z= 0.282 Chirality : 0.040 0.136 1182 Planarity : 0.004 0.055 1245 Dihedral : 10.827 83.713 1183 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.17 % Allowed : 18.22 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.27), residues: 946 helix: 0.96 (0.23), residues: 539 sheet: -1.18 (0.91), residues: 34 loop : -2.00 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 344 TYR 0.003 0.001 TYR C 91 PHE 0.014 0.001 PHE C 191 TRP 0.016 0.001 TRP C 44 HIS 0.003 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 7303) covalent geometry : angle 0.59382 / 0.28 ( 9921) hydrogen bonds : bond 0.02835 / 1.93 ( 304) hydrogen bonds : angle 3.39977 / 2.51 ( 912) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.171 Fit side-chains REVERT: C 19 ARG cc_start: 0.7257 (ptp90) cc_final: 0.6518 (pmt170) REVERT: C 93 ASP cc_start: 0.8232 (p0) cc_final: 0.7606 (p0) REVERT: C 150 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8501 (mp) REVERT: C 344 ARG cc_start: 0.8790 (mmm160) cc_final: 0.8451 (mmm160) REVERT: C 387 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: C 473 ARG cc_start: 0.7811 (ptt-90) cc_final: 0.7277 (ptt-90) REVERT: E 161 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7857 (mm-30) REVERT: D 131 LYS cc_start: 0.8953 (mtmt) cc_final: 0.8191 (mmtt) REVERT: D 171 GLU cc_start: 0.8537 (tp30) cc_final: 0.7977 (tt0) outliers start: 30 outliers final: 12 residues processed: 110 average time/residue: 0.4517 time to fit residues: 52.5252 Evaluate side-chains 106 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 59 optimal weight: 0.0570 chunk 32 optimal weight: 10.0000 chunk 90 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 79 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 193 HIS D 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.138031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113334 restraints weight = 8625.483| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.06 r_work: 0.3191 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7303 Z= 0.126 Angle : 0.600 14.538 9921 Z= 0.284 Chirality : 0.041 0.138 1182 Planarity : 0.004 0.056 1245 Dihedral : 10.657 83.002 1183 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.48 % Allowed : 19.33 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.27), residues: 946 helix: 1.04 (0.23), residues: 538 sheet: -1.21 (0.91), residues: 34 loop : -1.95 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 344 TYR 0.004 0.001 TYR D 86 PHE 0.015 0.001 PHE C 191 TRP 0.016 0.001 TRP C 44 HIS 0.002 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 7303) covalent geometry : angle 0.59989 / 0.28 ( 9921) hydrogen bonds : bond 0.02882 / 1.96 ( 304) hydrogen bonds : angle 3.39819 / 2.50 ( 912) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.263 Fit side-chains REVERT: C 19 ARG cc_start: 0.7283 (ptp90) cc_final: 0.6454 (pmt170) REVERT: C 93 ASP cc_start: 0.8250 (p0) cc_final: 0.7569 (p0) REVERT: C 125 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7471 (t70) REVERT: C 132 GLU cc_start: 0.7961 (tt0) cc_final: 0.7440 (mp0) REVERT: C 344 ARG cc_start: 0.8787 (mmm160) cc_final: 0.8414 (mmm160) REVERT: C 387 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7083 (tt0) REVERT: C 473 ARG cc_start: 0.7736 (ptt-90) cc_final: 0.7441 (ptt-90) REVERT: E 13 ARG cc_start: 0.7865 (ptp-110) cc_final: 0.7364 (mmt180) REVERT: E 67 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.6901 (tpm-80) REVERT: E 161 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7790 (mm-30) REVERT: D 131 LYS cc_start: 0.8920 (mtmt) cc_final: 0.8124 (mmtt) REVERT: D 171 GLU cc_start: 0.8573 (tp30) cc_final: 0.7944 (tt0) outliers start: 25 outliers final: 14 residues processed: 114 average time/residue: 0.5134 time to fit residues: 61.6298 Evaluate side-chains 110 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 18 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.0000 chunk 25 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 244 GLN E 193 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.137411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113225 restraints weight = 8614.683| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.01 r_work: 0.3193 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7303 Z= 0.120 Angle : 0.583 13.277 9921 Z= 0.280 Chirality : 0.041 0.137 1182 Planarity : 0.004 0.055 1245 Dihedral : 10.384 82.626 1183 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.62 % Allowed : 20.17 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.27), residues: 946 helix: 1.16 (0.23), residues: 538 sheet: -1.39 (0.88), residues: 34 loop : -1.87 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 67 TYR 0.003 0.001 TYR D 86 PHE 0.014 0.001 PHE C 191 TRP 0.016 0.001 TRP C 44 HIS 0.002 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 7303) covalent geometry : angle 0.58293 / 0.28 ( 9921) hydrogen bonds : bond 0.02795 / 1.90 ( 304) hydrogen bonds : angle 3.34020 / 2.47 ( 912) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.277 Fit side-chains REVERT: C 19 ARG cc_start: 0.7274 (ptp90) cc_final: 0.6464 (pmt170) REVERT: C 93 ASP cc_start: 0.8192 (p0) cc_final: 0.7584 (p0) REVERT: C 132 GLU cc_start: 0.7914 (tt0) cc_final: 0.7442 (mp0) REVERT: C 252 ARG cc_start: 0.8579 (mtm180) cc_final: 0.8030 (mtm180) REVERT: C 344 ARG cc_start: 0.8802 (mmm160) cc_final: 0.8357 (mmm160) REVERT: C 387 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: C 473 ARG cc_start: 0.7742 (ptt-90) cc_final: 0.7408 (ptt-90) REVERT: E 13 ARG cc_start: 0.7874 (ptp-110) cc_final: 0.7313 (mmt-90) REVERT: E 67 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.6781 (tpm-80) REVERT: E 161 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7803 (mm-30) REVERT: D 131 LYS cc_start: 0.8923 (mtmt) cc_final: 0.8136 (mmtt) REVERT: D 171 GLU cc_start: 0.8598 (tp30) cc_final: 0.8008 (tt0) outliers start: 26 outliers final: 15 residues processed: 113 average time/residue: 0.6223 time to fit residues: 74.0060 Evaluate side-chains 107 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 192 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 45 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 193 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.112968 restraints weight = 8644.697| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.05 r_work: 0.3179 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7303 Z= 0.132 Angle : 0.596 11.703 9921 Z= 0.286 Chirality : 0.041 0.140 1182 Planarity : 0.005 0.088 1245 Dihedral : 10.352 82.674 1183 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.76 % Allowed : 19.47 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.14 (0.27), residues: 946 helix: 1.14 (0.23), residues: 540 sheet: -1.47 (0.88), residues: 34 loop : -1.86 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 344 TYR 0.004 0.001 TYR D 86 PHE 0.015 0.001 PHE C 191 TRP 0.016 0.001 TRP C 44 HIS 0.002 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 ( 7303) covalent geometry : angle 0.59614 / 0.29 ( 9921) hydrogen bonds : bond 0.02866 / 1.95 ( 304) hydrogen bonds : angle 3.35898 / 2.48 ( 912) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: C 19 ARG cc_start: 0.7300 (ptp90) cc_final: 0.6444 (pmt170) REVERT: C 93 ASP cc_start: 0.8231 (p0) cc_final: 0.7574 (p0) REVERT: C 125 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7423 (t70) REVERT: C 299 GLU cc_start: 0.7906 (pt0) cc_final: 0.7678 (pt0) REVERT: C 344 ARG cc_start: 0.8798 (mmm160) cc_final: 0.8287 (mmm160) REVERT: C 387 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: C 473 ARG cc_start: 0.7759 (ptt-90) cc_final: 0.7416 (ptt-90) REVERT: E 13 ARG cc_start: 0.7906 (ptp-110) cc_final: 0.7350 (mmt-90) REVERT: E 67 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.6831 (tpm-80) REVERT: E 161 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7772 (mm-30) REVERT: D 131 LYS cc_start: 0.8898 (mtmt) cc_final: 0.8090 (mmtt) REVERT: D 171 GLU cc_start: 0.8624 (tp30) cc_final: 0.7998 (tt0) outliers start: 27 outliers final: 18 residues processed: 108 average time/residue: 0.6146 time to fit residues: 69.8268 Evaluate side-chains 108 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 192 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 86 optimal weight: 0.0670 chunk 28 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 73 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 244 GLN E 193 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.114454 restraints weight = 8427.010| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.99 r_work: 0.3209 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7303 Z= 0.113 Angle : 0.566 10.330 9921 Z= 0.274 Chirality : 0.041 0.135 1182 Planarity : 0.005 0.076 1245 Dihedral : 10.209 82.639 1183 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.34 % Allowed : 20.45 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.27), residues: 946 helix: 1.24 (0.23), residues: 540 sheet: -1.40 (0.89), residues: 34 loop : -1.84 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 33 TYR 0.004 0.001 TYR C 91 PHE 0.014 0.001 PHE C 191 TRP 0.016 0.001 TRP C 44 HIS 0.002 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.11 ( 7303) covalent geometry : angle 0.56552 / 0.27 ( 9921) hydrogen bonds : bond 0.02733 / 1.86 ( 304) hydrogen bonds : angle 3.29065 / 2.43 ( 912) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: C 19 ARG cc_start: 0.7305 (ptp90) cc_final: 0.6461 (pmt170) REVERT: C 67 ARG cc_start: 0.7300 (ttt90) cc_final: 0.7041 (ttt180) REVERT: C 93 ASP cc_start: 0.8196 (p0) cc_final: 0.7588 (p0) REVERT: C 299 GLU cc_start: 0.7850 (pt0) cc_final: 0.7614 (pt0) REVERT: C 344 ARG cc_start: 0.8791 (mmm160) cc_final: 0.8263 (mmm160) REVERT: C 387 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7296 (tt0) REVERT: C 422 LEU cc_start: 0.8437 (mm) cc_final: 0.8197 (mp) REVERT: C 473 ARG cc_start: 0.7738 (ptt-90) cc_final: 0.7281 (ptt-90) REVERT: E 13 ARG cc_start: 0.7816 (ptp-110) cc_final: 0.7355 (mmt180) REVERT: E 67 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.6788 (tpm-80) REVERT: E 161 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7782 (mm-30) REVERT: D 131 LYS cc_start: 0.8894 (mtmt) cc_final: 0.8117 (mmtt) REVERT: D 171 GLU cc_start: 0.8582 (tp30) cc_final: 0.7993 (tt0) outliers start: 24 outliers final: 17 residues processed: 107 average time/residue: 0.6097 time to fit residues: 68.6963 Evaluate side-chains 112 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 192 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 48 optimal weight: 0.1980 chunk 85 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 193 HIS D 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.136689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.112593 restraints weight = 8521.362| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.99 r_work: 0.3194 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7303 Z= 0.135 Angle : 0.588 10.785 9921 Z= 0.285 Chirality : 0.041 0.141 1182 Planarity : 0.005 0.071 1245 Dihedral : 10.233 82.912 1183 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.92 % Allowed : 21.00 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.16 (0.27), residues: 946 helix: 1.10 (0.23), residues: 546 sheet: -1.54 (0.88), residues: 34 loop : -1.87 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 223 TYR 0.004 0.001 TYR C 91 PHE 0.016 0.001 PHE C 191 TRP 0.016 0.001 TRP C 44 HIS 0.002 0.001 HIS C 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 7303) covalent geometry : angle 0.58815 / 0.28 ( 9921) hydrogen bonds : bond 0.02874 / 1.96 ( 304) hydrogen bonds : angle 3.34778 / 2.48 ( 912) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: C 19 ARG cc_start: 0.7294 (ptp90) cc_final: 0.6423 (pmt170) REVERT: C 67 ARG cc_start: 0.7325 (ttt90) cc_final: 0.7123 (tpt170) REVERT: C 93 ASP cc_start: 0.8204 (p0) cc_final: 0.7528 (p0) REVERT: C 132 GLU cc_start: 0.7896 (tt0) cc_final: 0.7324 (mp0) REVERT: C 344 ARG cc_start: 0.8771 (mmm160) cc_final: 0.8238 (mmm160) REVERT: C 387 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: C 473 ARG cc_start: 0.7808 (ptt-90) cc_final: 0.7331 (ptt-90) REVERT: E 13 ARG cc_start: 0.7848 (ptp-110) cc_final: 0.7317 (mmt-90) REVERT: E 67 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.6884 (tpm-80) REVERT: E 161 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7798 (mm-30) REVERT: D 131 LYS cc_start: 0.8892 (mtmt) cc_final: 0.8107 (mmtt) REVERT: D 171 GLU cc_start: 0.8595 (tp30) cc_final: 0.8004 (tt0) outliers start: 21 outliers final: 17 residues processed: 106 average time/residue: 0.6370 time to fit residues: 71.0120 Evaluate side-chains 110 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 192 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 27 optimal weight: 0.0170 chunk 67 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 52 optimal weight: 0.0030 chunk 91 optimal weight: 0.9980 overall best weight: 0.3828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 193 HIS D 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.138437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.114337 restraints weight = 8466.610| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.99 r_work: 0.3208 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 7303 Z= 0.110 Angle : 0.562 10.555 9921 Z= 0.272 Chirality : 0.040 0.134 1182 Planarity : 0.004 0.062 1245 Dihedral : 10.071 83.035 1183 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.92 % Allowed : 21.28 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.28), residues: 946 helix: 1.24 (0.23), residues: 546 sheet: -1.54 (0.89), residues: 34 loop : -1.77 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 344 TYR 0.005 0.001 TYR C 91 PHE 0.014 0.001 PHE C 191 TRP 0.015 0.001 TRP C 44 HIS 0.002 0.001 HIS C 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 7303) covalent geometry : angle 0.56170 / 0.27 ( 9921) hydrogen bonds : bond 0.02708 / 1.85 ( 304) hydrogen bonds : angle 3.27336 / 2.42 ( 912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2304.44 seconds wall clock time: 39 minutes 59.40 seconds (2399.40 seconds total)