Starting phenix.real_space_refine on Fri Aug 22 19:14:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1n_36796/08_2025/8k1n_36796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1n_36796/08_2025/8k1n_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_2025/8k1n_36796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1n_36796/08_2025/8k1n_36796.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1n_36796/08_2025/8k1n_36796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1n_36796/08_2025/8k1n_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-2.0-5787/lib/python3.9/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: 1.96, per 1000 atoms: 0.27 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: 0.65 Conformation dependent library (CDL) restraints added in 425.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.11 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: 0.79 Time building geometry restraints manager: 0.84 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 - 2.27: 9270 2.27 - 4.54: 495 4.54 - 6.81: 102 6.81 - 9.07: 46 9.07 - 11.34: 8 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: 3842 17.25 - 34.50: 380 34.50 - 51.75: 88 51.75 - 69.00: 34 69.00 - 86.25: 6 Dihedral angle restraints: 4350 sinusoidal: 1706 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 4347 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: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.690 Find NCS groups from input model: 0.050 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:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 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= 0.529 Angle : 1.239 11.343 9921 Z= 0.806 Chirality : 0.066 0.458 1182 Planarity : 0.015 0.252 1245 Dihedral : 15.248 86.254 2670 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 aren 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 covalent geometry : bond 0.00810 ( 7303) covalent geometry : angle 1.23876 ( 9921) hydrogen bonds : bond 0.14881 ( 304) hydrogen bonds : angle 6.19566 ( 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 : 0.179 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: 0.5133 time to fit residues: 80.0692 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 : 0.172 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3679 r_free = 0.3679 target = 0.143660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118991 restraints weight = 8678.230| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.09 r_work: 0.3256 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 7303 Z= 0.148 Angle : 0.715 18.579 9921 Z= 0.340 Chirality : 0.044 0.201 1182 Planarity : 0.005 0.068 1245 Dihedral : 13.085 123.198 1167 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.76 % Allowed : 10.99 % Favored : 85.26 % 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 aren not related in a simple way. whole: -1.20 (0.27), residues: 946 helix: 0.26 (0.23), residues: 541 sheet: -1.11 (0.74), residues: 58 loop : -2.43 (0.29), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 33 TYR 0.007 0.001 TYR C 56 PHE 0.020 0.002 PHE C 365 TRP 0.019 0.001 TRP C 44 HIS 0.004 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 7303) covalent geometry : angle 0.71512 ( 9921) hydrogen bonds : bond 0.03535 ( 304) hydrogen bonds : angle 3.84326 ( 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 132 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.159 Fit side-chains REVERT: C 78 MET cc_start: 0.7894 (mmm) cc_final: 0.7693 (mmm) REVERT: C 93 ASP cc_start: 0.8278 (p0) cc_final: 0.7595 (p0) REVERT: C 125 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7434 (t70) REVERT: C 387 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7294 (tt0) REVERT: C 488 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7841 (tp) REVERT: E 161 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7607 (mm-30) REVERT: E 204 LYS cc_start: 0.7714 (mttp) cc_final: 0.7473 (ttmm) REVERT: D 128 ASP cc_start: 0.7995 (t0) cc_final: 0.7638 (t70) REVERT: D 131 LYS cc_start: 0.8617 (mtmt) cc_final: 0.7823 (mmtt) REVERT: D 171 GLU cc_start: 0.8428 (tp30) cc_final: 0.7774 (tt0) REVERT: D 209 ARG cc_start: 0.7251 (ttm170) cc_final: 0.6268 (tpm170) outliers start: 27 outliers final: 8 residues processed: 117 average time/residue: 0.5417 time to fit residues: 66.2223 Evaluate side-chains 112 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 7 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 48 optimal weight: 0.0070 chunk 12 optimal weight: 0.0980 chunk 52 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.143489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.119395 restraints weight = 8531.029| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.00 r_work: 0.3273 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2106 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= 0.109 Angle : 0.628 15.123 9921 Z= 0.294 Chirality : 0.041 0.148 1182 Planarity : 0.005 0.057 1245 Dihedral : 11.841 106.712 1167 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.03 % Allowed : 14.60 % Favored : 81.36 % 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 aren not related in a simple way. whole: -0.70 (0.27), residues: 946 helix: 0.65 (0.23), residues: 538 sheet: -0.12 (1.20), residues: 24 loop : -2.16 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 344 TYR 0.005 0.001 TYR C 56 PHE 0.014 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 covalent geometry : bond 0.00257 ( 7303) covalent geometry : angle 0.62786 ( 9921) hydrogen bonds : bond 0.03013 ( 304) hydrogen bonds : angle 3.51351 ( 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 133 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: C 67 ARG cc_start: 0.7361 (ttt90) cc_final: 0.7081 (ttt90) REVERT: C 93 ASP cc_start: 0.8257 (p0) cc_final: 0.7518 (p0) REVERT: C 296 MET cc_start: 0.8299 (mmm) cc_final: 0.8099 (mtp) REVERT: C 488 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7831 (tp) REVERT: E 161 GLU cc_start: 0.8458 (mt-10) cc_final: 0.7618 (mm-30) REVERT: D 34 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7248 (mt-10) REVERT: D 131 LYS cc_start: 0.8712 (mtmt) cc_final: 0.7983 (mmtt) REVERT: D 171 GLU cc_start: 0.8404 (tp30) cc_final: 0.7805 (tt0) REVERT: D 183 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7373 (mt0) outliers start: 29 outliers final: 13 residues processed: 116 average time/residue: 0.4902 time to fit residues: 59.5929 Evaluate side-chains 107 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 170 MET 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 34 GLU Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 183 GLN Chi-restraints excluded: chain D residue 202 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 68 optimal weight: 0.0370 chunk 41 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.116215 restraints weight = 8651.058| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.09 r_work: 0.3224 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2429 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= 0.130 Angle : 0.615 15.445 9921 Z= 0.292 Chirality : 0.041 0.142 1182 Planarity : 0.005 0.055 1245 Dihedral : 11.093 89.271 1167 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.31 % Allowed : 16.69 % Favored : 79.00 % 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 aren not related in a simple way. whole: -0.61 (0.27), residues: 946 helix: 0.74 (0.23), residues: 544 sheet: -0.36 (1.19), residues: 24 loop : -2.17 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 344 TYR 0.007 0.001 TYR C 248 PHE 0.016 0.001 PHE C 191 TRP 0.016 0.001 TRP C 44 HIS 0.003 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7303) covalent geometry : angle 0.61549 ( 9921) hydrogen bonds : bond 0.03005 ( 304) hydrogen bonds : angle 3.46521 ( 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 127 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.218 Fit side-chains REVERT: C 93 ASP cc_start: 0.8305 (p0) cc_final: 0.7645 (p0) REVERT: C 102 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8852 (ttpt) REVERT: C 125 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7544 (t70) REVERT: C 283 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8224 (tp) REVERT: C 350 MET cc_start: 0.6828 (OUTLIER) cc_final: 0.6193 (ptt) REVERT: C 473 ARG cc_start: 0.7764 (ptt-90) cc_final: 0.7237 (ptt-90) REVERT: C 488 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8124 (tt) REVERT: C 505 GLU cc_start: 0.7939 (pt0) cc_final: 0.7734 (pt0) REVERT: E 161 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7720 (mm-30) REVERT: E 206 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8431 (t) REVERT: D 131 LYS cc_start: 0.8844 (mtmt) cc_final: 0.8050 (mmtt) REVERT: D 171 GLU cc_start: 0.8490 (tp30) cc_final: 0.7873 (tt0) REVERT: D 183 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7494 (mt0) outliers start: 31 outliers final: 9 residues processed: 111 average time/residue: 0.4799 time to fit residues: 55.9875 Evaluate side-chains 102 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 102 LYS Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 350 MET 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 E residue 25 LEU Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 206 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 55 optimal weight: 0.0770 chunk 7 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 48 optimal weight: 0.0040 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 54 optimal weight: 0.0770 overall best weight: 0.3708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 HIS E 38 HIS E 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.141542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116739 restraints weight = 8567.648| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.03 r_work: 0.3238 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 7303 Z= 0.109 Angle : 0.590 15.001 9921 Z= 0.279 Chirality : 0.040 0.136 1182 Planarity : 0.004 0.055 1245 Dihedral : 10.463 81.920 1167 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.03 % Allowed : 18.50 % Favored : 77.47 % 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 aren not related in a simple way. whole: -0.25 (0.27), residues: 946 helix: 1.04 (0.23), residues: 539 sheet: -0.60 (1.12), residues: 24 loop : -1.96 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 344 TYR 0.007 0.001 TYR C 248 PHE 0.013 0.001 PHE C 191 TRP 0.016 0.001 TRP C 44 HIS 0.003 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7303) covalent geometry : angle 0.59034 ( 9921) hydrogen bonds : bond 0.02725 ( 304) hydrogen bonds : angle 3.34203 ( 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 128 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.275 Fit side-chains REVERT: C 93 ASP cc_start: 0.8242 (p0) cc_final: 0.7568 (p0) REVERT: C 102 LYS cc_start: 0.9152 (ttpp) cc_final: 0.8941 (ttpp) REVERT: C 473 ARG cc_start: 0.7713 (ptt-90) cc_final: 0.7159 (ptt-90) REVERT: C 488 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8116 (tt) REVERT: E 13 ARG cc_start: 0.7474 (ptp-110) cc_final: 0.7268 (mmt-90) REVERT: E 161 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7743 (mm-30) REVERT: E 206 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8508 (t) REVERT: D 131 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8090 (mmtt) REVERT: D 171 GLU cc_start: 0.8477 (tp30) cc_final: 0.7893 (tt0) outliers start: 29 outliers final: 11 residues processed: 115 average time/residue: 0.5092 time to fit residues: 61.6835 Evaluate side-chains 104 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 333 ILE Chi-restraints excluded: chain C residue 356 LEU 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 D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3582 r_free = 0.3582 target = 0.135194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110582 restraints weight = 8648.188| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.02 r_work: 0.3150 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7303 Z= 0.192 Angle : 0.649 14.786 9921 Z= 0.312 Chirality : 0.044 0.157 1182 Planarity : 0.005 0.058 1245 Dihedral : 10.488 78.386 1167 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.76 % Allowed : 20.17 % 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 aren not related in a simple way. whole: -0.50 (0.27), residues: 946 helix: 0.79 (0.23), residues: 546 sheet: -1.24 (0.89), residues: 34 loop : -1.99 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 344 TYR 0.008 0.001 TYR C 248 PHE 0.019 0.002 PHE C 191 TRP 0.016 0.001 TRP C 44 HIS 0.004 0.001 HIS C 404 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 7303) covalent geometry : angle 0.64850 ( 9921) hydrogen bonds : bond 0.03284 ( 304) hydrogen bonds : angle 3.54457 ( 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 119 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: C 19 ARG cc_start: 0.7271 (ptp90) cc_final: 0.6473 (pmt170) REVERT: C 93 ASP cc_start: 0.8245 (p0) cc_final: 0.7602 (p0) REVERT: C 102 LYS cc_start: 0.9184 (ttpp) cc_final: 0.8922 (ttpt) REVERT: C 473 ARG cc_start: 0.7905 (ptt-90) cc_final: 0.7620 (ptt-90) REVERT: C 488 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8104 (tt) REVERT: E 13 ARG cc_start: 0.7737 (ptp-110) cc_final: 0.7311 (mmt-90) REVERT: E 161 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7752 (mm-30) REVERT: D 131 LYS cc_start: 0.8935 (mtmt) cc_final: 0.8141 (mmtt) REVERT: D 171 GLU cc_start: 0.8586 (tp30) cc_final: 0.8027 (tt0) REVERT: D 209 ARG cc_start: 0.7179 (ttm170) cc_final: 0.5974 (mmp80) outliers start: 27 outliers final: 18 residues processed: 108 average time/residue: 0.5102 time to fit residues: 57.9928 Evaluate side-chains 107 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 356 LEU 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 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 192 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 18 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 193 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.111064 restraints weight = 8635.082| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.02 r_work: 0.3165 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7303 Z= 0.157 Angle : 0.618 13.664 9921 Z= 0.298 Chirality : 0.042 0.146 1182 Planarity : 0.005 0.057 1245 Dihedral : 10.214 77.920 1167 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.89 % Allowed : 20.03 % 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 aren not related in a simple way. whole: -0.45 (0.27), residues: 946 helix: 0.84 (0.22), residues: 546 sheet: -1.59 (0.83), residues: 34 loop : -1.96 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 344 TYR 0.008 0.001 TYR C 248 PHE 0.016 0.001 PHE C 191 TRP 0.016 0.001 TRP C 44 HIS 0.003 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 7303) covalent geometry : angle 0.61804 ( 9921) hydrogen bonds : bond 0.03075 ( 304) hydrogen bonds : angle 3.49931 ( 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: 28 poor density : 94 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: C 19 ARG cc_start: 0.7295 (ptp90) cc_final: 0.6421 (pmt170) REVERT: C 93 ASP cc_start: 0.8242 (p0) cc_final: 0.7591 (p0) REVERT: C 102 LYS cc_start: 0.9193 (ttpp) cc_final: 0.8962 (ttpt) REVERT: C 125 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7603 (t70) REVERT: C 324 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8329 (tt) REVERT: C 473 ARG cc_start: 0.7881 (ptt-90) cc_final: 0.7580 (ptt-90) REVERT: C 488 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8129 (tt) REVERT: E 161 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7769 (mm-30) REVERT: D 131 LYS cc_start: 0.8916 (mtmt) cc_final: 0.8137 (mmtt) REVERT: D 171 GLU cc_start: 0.8598 (tp30) cc_final: 0.8033 (tt0) REVERT: D 209 ARG cc_start: 0.7214 (ttm170) cc_final: 0.6013 (mmp80) outliers start: 28 outliers final: 17 residues processed: 111 average time/residue: 0.5107 time to fit residues: 59.5583 Evaluate side-chains 115 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 356 LEU 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 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 212 LYS Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 25 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: 0.0980 chunk 23 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 193 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.136275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111782 restraints weight = 8653.414| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.02 r_work: 0.3171 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3087 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= 0.139 Angle : 0.603 12.739 9921 Z= 0.292 Chirality : 0.042 0.142 1182 Planarity : 0.005 0.079 1245 Dihedral : 9.922 76.346 1167 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.89 % Allowed : 20.31 % 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 aren not related in a simple way. whole: -0.26 (0.27), residues: 946 helix: 1.02 (0.23), residues: 539 sheet: -1.48 (0.86), residues: 34 loop : -1.87 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 344 TYR 0.009 0.001 TYR C 248 PHE 0.016 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 covalent geometry : bond 0.00342 ( 7303) covalent geometry : angle 0.60290 ( 9921) hydrogen bonds : bond 0.02973 ( 304) hydrogen bonds : angle 3.44208 ( 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 125 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: C 19 ARG cc_start: 0.7276 (ptp90) cc_final: 0.6418 (pmt170) REVERT: C 93 ASP cc_start: 0.8256 (p0) cc_final: 0.7618 (p0) REVERT: C 125 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7466 (t70) REVERT: C 252 ARG cc_start: 0.8631 (mtm180) cc_final: 0.8059 (mtm180) REVERT: C 473 ARG cc_start: 0.7859 (ptt-90) cc_final: 0.7520 (ptt-90) REVERT: E 13 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7398 (mtt-85) REVERT: E 161 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7718 (mm-30) REVERT: D 131 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8120 (mmtt) REVERT: D 171 GLU cc_start: 0.8597 (tp30) cc_final: 0.8032 (tt0) outliers start: 28 outliers final: 18 residues processed: 114 average time/residue: 0.4814 time to fit residues: 57.7558 Evaluate side-chains 112 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 356 LEU 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 13 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 198 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 86 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.0000 chunk 73 optimal weight: 0.0370 chunk 19 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 overall best weight: 0.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3615 r_free = 0.3615 target = 0.137828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113413 restraints weight = 8477.219| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.00 r_work: 0.3195 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3188 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= 0.118 Angle : 0.595 11.517 9921 Z= 0.285 Chirality : 0.041 0.135 1182 Planarity : 0.005 0.071 1245 Dihedral : 9.677 73.805 1167 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.78 % Allowed : 21.42 % 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 aren not related in a simple way. whole: -0.12 (0.27), residues: 946 helix: 1.15 (0.23), residues: 538 sheet: -1.29 (0.91), residues: 34 loop : -1.85 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 344 TYR 0.008 0.001 TYR C 248 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 covalent geometry : bond 0.00287 ( 7303) covalent geometry : angle 0.59490 ( 9921) hydrogen bonds : bond 0.02805 ( 304) hydrogen bonds : angle 3.35667 ( 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 111 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.177 Fit side-chains REVERT: C 19 ARG cc_start: 0.7290 (ptp90) cc_final: 0.6439 (pmt170) REVERT: C 93 ASP cc_start: 0.8202 (p0) cc_final: 0.7521 (p0) REVERT: C 125 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7479 (t70) REVERT: C 132 GLU cc_start: 0.7627 (tt0) cc_final: 0.7163 (mp0) REVERT: C 252 ARG cc_start: 0.8573 (mtm180) cc_final: 0.8029 (mtm180) REVERT: C 299 GLU cc_start: 0.7932 (pt0) cc_final: 0.7715 (pt0) REVERT: C 324 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8246 (tt) REVERT: C 473 ARG cc_start: 0.7770 (ptt-90) cc_final: 0.7441 (ptt-90) REVERT: E 13 ARG cc_start: 0.7771 (ptp-110) cc_final: 0.7418 (mmt180) REVERT: E 161 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7667 (mm-30) REVERT: D 131 LYS cc_start: 0.8909 (mtmt) cc_final: 0.8120 (mmtt) REVERT: D 171 GLU cc_start: 0.8596 (tp30) cc_final: 0.8001 (tt0) outliers start: 20 outliers final: 15 residues processed: 105 average time/residue: 0.4679 time to fit residues: 51.7517 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 : 0.148 ------------------------------------------------------------------------------- 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 311 SER Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 212 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.3793 > 50: distance: 61 - 70: 28.538 distance: 70 - 71: 33.840 distance: 70 - 76: 37.242 distance: 71 - 72: 33.594 distance: 71 - 74: 3.843 distance: 72 - 73: 41.434 distance: 72 - 77: 38.115 distance: 74 - 75: 39.651 distance: 75 - 76: 68.379 distance: 77 - 78: 22.363 distance: 78 - 79: 35.445 distance: 78 - 81: 39.776 distance: 79 - 80: 42.279 distance: 79 - 86: 21.889 distance: 81 - 82: 13.479 distance: 82 - 83: 19.745 distance: 83 - 84: 12.363 distance: 83 - 85: 13.485 distance: 86 - 87: 11.858 distance: 87 - 88: 26.935 distance: 87 - 90: 33.270 distance: 88 - 89: 21.804 distance: 88 - 94: 44.042 distance: 90 - 91: 39.508 distance: 91 - 92: 44.644 distance: 92 - 93: 29.483 distance: 94 - 95: 12.116 distance: 95 - 96: 41.429 distance: 95 - 98: 40.069 distance: 96 - 97: 37.694 distance: 96 - 102: 18.895 distance: 98 - 99: 38.198 distance: 99 - 100: 25.226 distance: 99 - 101: 24.122 distance: 102 - 103: 24.565 distance: 103 - 104: 37.464 distance: 103 - 106: 30.915 distance: 104 - 105: 10.552 distance: 104 - 110: 15.526 distance: 107 - 108: 43.237 distance: 107 - 109: 54.984 distance: 110 - 111: 36.087 distance: 111 - 112: 44.865 distance: 111 - 114: 37.237 distance: 112 - 113: 23.370 distance: 112 - 118: 11.428 distance: 114 - 115: 39.017 distance: 115 - 116: 44.554 distance: 115 - 117: 33.536 distance: 118 - 119: 25.981 distance: 119 - 120: 26.002 distance: 119 - 122: 15.273 distance: 120 - 121: 12.180 distance: 120 - 126: 19.746 distance: 122 - 123: 28.567 distance: 123 - 124: 29.802 distance: 123 - 125: 41.891 distance: 127 - 128: 17.979 distance: 127 - 130: 23.770 distance: 128 - 129: 22.478 distance: 128 - 135: 19.281 distance: 130 - 131: 21.309 distance: 131 - 132: 27.431 distance: 132 - 133: 12.167 distance: 132 - 134: 15.739 distance: 135 - 136: 15.006 distance: 135 - 141: 24.246 distance: 136 - 137: 18.296 distance: 136 - 139: 20.298 distance: 137 - 138: 16.619 distance: 137 - 142: 33.048 distance: 139 - 140: 32.245 distance: 140 - 141: 19.197 distance: 142 - 143: 37.424 distance: 143 - 144: 9.987 distance: 143 - 146: 37.290 distance: 144 - 145: 18.347 distance: 144 - 153: 33.137 distance: 146 - 147: 46.336 distance: 147 - 148: 21.918 distance: 147 - 149: 28.572 distance: 148 - 150: 21.971 distance: 149 - 151: 28.957 distance: 150 - 152: 15.768 distance: 151 - 152: 15.686