Starting phenix.real_space_refine on Sun May 11 00:34:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1n_36796/05_2025/8k1n_36796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1n_36796/05_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_36796/05_2025/8k1n_36796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1n_36796/05_2025/8k1n_36796.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1n_36796/05_2025/8k1n_36796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1n_36796/05_2025/8k1n_36796.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.070 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.28, per 1000 atoms: 0.74 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: 2.08 Conformation dependent library (CDL) restraints added in 809.9 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: 0.57 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: 1.60 Time building geometry restraints manager: 2.27 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: 3.800 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.450 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.450 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (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 TRP 0.017 0.001 TRP C 44 HIS 0.011 0.002 HIS E 153 PHE 0.027 0.003 PHE E 19 TYR 0.026 0.002 TYR C 56 ARG 0.012 0.001 ARG C 544 Details of bonding type rmsd hydrogen bonds : bond 0.14881 ( 304) hydrogen bonds : angle 6.19566 ( 912) covalent geometry : bond 0.00810 ( 7303) covalent geometry : angle 1.23876 ( 9921) *********************** 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 : 0.680 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: 1.3501 time to fit residues: 210.9238 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 : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 2.9990 chunk 72 optimal weight: 0.0000 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 55 optimal weight: 0.0170 chunk 86 optimal weight: 0.4980 overall best weight: 0.3822 ------------------------------------------------------------------------------- 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 193 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.145235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.121705 restraints weight = 8539.028| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.99 r_work: 0.3292 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1562 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= 0.127 Angle : 0.697 17.328 9921 Z= 0.331 Chirality : 0.043 0.183 1182 Planarity : 0.005 0.067 1245 Dihedral : 13.042 126.287 1167 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.48 % Allowed : 11.13 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.27), residues: 946 helix: 0.28 (0.23), residues: 544 sheet: -1.09 (0.74), residues: 58 loop : -2.44 (0.29), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 44 HIS 0.003 0.001 HIS E 18 PHE 0.019 0.001 PHE C 365 TYR 0.008 0.001 TYR C 56 ARG 0.008 0.000 ARG D 33 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 304) hydrogen bonds : angle 3.79210 ( 912) covalent geometry : bond 0.00298 ( 7303) covalent geometry : angle 0.69678 ( 9921) *********************** 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 130 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.710 Fit side-chains REVERT: C 93 ASP cc_start: 0.8269 (p0) cc_final: 0.7636 (p0) REVERT: C 488 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7922 (tp) REVERT: E 30 LEU cc_start: 0.8471 (mp) cc_final: 0.8231 (mm) REVERT: E 161 GLU cc_start: 0.8421 (mt-10) cc_final: 0.7638 (mm-30) REVERT: D 128 ASP cc_start: 0.7888 (t0) cc_final: 0.7527 (t70) REVERT: D 131 LYS cc_start: 0.8528 (mtmt) cc_final: 0.7810 (mmtt) REVERT: D 171 GLU cc_start: 0.8370 (tp30) cc_final: 0.7779 (tt0) REVERT: D 209 ARG cc_start: 0.7227 (ttm170) cc_final: 0.6299 (tpm170) outliers start: 25 outliers final: 8 residues processed: 116 average time/residue: 1.4076 time to fit residues: 171.1081 Evaluate side-chains 101 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 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 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 32 optimal weight: 0.0010 chunk 59 optimal weight: 0.0070 chunk 92 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 0.0030 chunk 48 optimal weight: 0.7980 chunk 88 optimal weight: 0.0970 overall best weight: 0.1612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.146806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123234 restraints weight = 8589.523| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.00 r_work: 0.3320 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 7303 Z= 0.099 Angle : 0.615 14.979 9921 Z= 0.287 Chirality : 0.040 0.145 1182 Planarity : 0.004 0.054 1245 Dihedral : 11.623 103.285 1167 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.03 % Allowed : 14.05 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.27), residues: 946 helix: 0.77 (0.23), residues: 538 sheet: -1.30 (0.96), residues: 36 loop : -2.11 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 44 HIS 0.002 0.001 HIS C 409 PHE 0.012 0.001 PHE C 191 TYR 0.006 0.001 TYR C 56 ARG 0.015 0.000 ARG C 344 Details of bonding type rmsd hydrogen bonds : bond 0.02856 ( 304) hydrogen bonds : angle 3.43784 ( 912) covalent geometry : bond 0.00230 ( 7303) covalent geometry : angle 0.61464 ( 9921) *********************** 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 130 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: C 67 ARG cc_start: 0.7331 (ttt90) cc_final: 0.7062 (ttt90) REVERT: C 93 ASP cc_start: 0.8257 (p0) cc_final: 0.7541 (p0) REVERT: C 125 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7458 (t70) REVERT: C 344 ARG cc_start: 0.8729 (mmm160) cc_final: 0.8517 (mmm160) REVERT: C 488 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7866 (tp) REVERT: E 161 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7670 (mm-30) REVERT: D 34 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.7057 (mt-10) REVERT: D 128 ASP cc_start: 0.7977 (t0) cc_final: 0.7756 (t70) REVERT: D 131 LYS cc_start: 0.8630 (mtmt) cc_final: 0.7938 (mmtt) REVERT: D 171 GLU cc_start: 0.8347 (tp30) cc_final: 0.7740 (tt0) REVERT: D 183 GLN cc_start: 0.7560 (pt0) cc_final: 0.7228 (mt0) outliers start: 29 outliers final: 10 residues processed: 111 average time/residue: 1.3680 time to fit residues: 159.4373 Evaluate side-chains 107 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 423 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 512 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 34 GLU Chi-restraints excluded: chain D residue 123 GLU 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 45 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 21 optimal weight: 0.0030 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.140075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.115437 restraints weight = 8630.079| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.03 r_work: 0.3228 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2510 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= 0.136 Angle : 0.617 15.696 9921 Z= 0.294 Chirality : 0.041 0.145 1182 Planarity : 0.005 0.058 1245 Dihedral : 10.819 83.563 1167 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.73 % Allowed : 15.72 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.27), residues: 946 helix: 0.82 (0.23), residues: 543 sheet: -0.42 (1.19), residues: 24 loop : -2.13 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 44 HIS 0.003 0.001 HIS E 18 PHE 0.016 0.002 PHE C 191 TYR 0.006 0.001 TYR C 248 ARG 0.007 0.000 ARG C 344 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 304) hydrogen bonds : angle 3.43086 ( 912) covalent geometry : bond 0.00329 ( 7303) covalent geometry : angle 0.61718 ( 9921) *********************** 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 130 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: C 93 ASP cc_start: 0.8308 (p0) cc_final: 0.7666 (p0) REVERT: C 102 LYS cc_start: 0.9181 (ttpp) cc_final: 0.8941 (ttpp) REVERT: C 283 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8160 (tp) REVERT: C 344 ARG cc_start: 0.8786 (mmm160) cc_final: 0.8481 (mmm160) REVERT: C 473 ARG cc_start: 0.7765 (ptt-90) cc_final: 0.7232 (ptt-90) REVERT: C 488 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8118 (tt) REVERT: E 161 GLU cc_start: 0.8509 (mt-10) cc_final: 0.7789 (mm-30) REVERT: E 206 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8480 (t) REVERT: D 13 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6533 (mmp80) REVERT: D 131 LYS cc_start: 0.8807 (mtmt) cc_final: 0.8066 (mmtt) REVERT: D 171 GLU cc_start: 0.8504 (tp30) cc_final: 0.7891 (tt0) REVERT: D 183 GLN cc_start: 0.7695 (pt0) cc_final: 0.7481 (mt0) outliers start: 34 outliers final: 10 residues processed: 115 average time/residue: 1.2771 time to fit residues: 154.4701 Evaluate side-chains 103 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 333 ILE 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 198 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.0010 chunk 82 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 72 optimal weight: 0.0070 chunk 80 optimal weight: 0.0050 chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 0.0670 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 overall best weight: 0.0556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.146529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.122190 restraints weight = 8417.433| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.02 r_work: 0.3307 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 7303 Z= 0.093 Angle : 0.563 15.155 9921 Z= 0.265 Chirality : 0.039 0.128 1182 Planarity : 0.004 0.052 1245 Dihedral : 10.089 76.374 1167 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.34 % Allowed : 18.78 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.28), residues: 946 helix: 1.21 (0.23), residues: 539 sheet: -0.37 (1.22), residues: 24 loop : -1.92 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 44 HIS 0.002 0.001 HIS D 38 PHE 0.009 0.001 PHE C 191 TYR 0.005 0.001 TYR C 56 ARG 0.003 0.000 ARG D 33 Details of bonding type rmsd hydrogen bonds : bond 0.02508 ( 304) hydrogen bonds : angle 3.20420 ( 912) covalent geometry : bond 0.00215 ( 7303) covalent geometry : angle 0.56348 ( 9921) *********************** 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 116 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: C 93 ASP cc_start: 0.8233 (p0) cc_final: 0.7608 (p0) REVERT: C 102 LYS cc_start: 0.9103 (ttpp) cc_final: 0.8880 (ttpp) REVERT: C 344 ARG cc_start: 0.8761 (mmm160) cc_final: 0.8466 (mmm160) REVERT: C 422 LEU cc_start: 0.8344 (mm) cc_final: 0.8119 (mp) REVERT: C 473 ARG cc_start: 0.7578 (ptt-90) cc_final: 0.7064 (ptt-90) REVERT: E 161 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7698 (mm-30) REVERT: E 206 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8335 (t) REVERT: D 131 LYS cc_start: 0.8775 (mtmt) cc_final: 0.8042 (mmtt) REVERT: D 171 GLU cc_start: 0.8408 (tp30) cc_final: 0.7802 (tt0) outliers start: 24 outliers final: 8 residues processed: 104 average time/residue: 1.1889 time to fit residues: 130.6043 Evaluate side-chains 92 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 512 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 206 THR 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 5 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 86 optimal weight: 0.0070 chunk 55 optimal weight: 0.6980 chunk 56 optimal weight: 0.0060 chunk 58 optimal weight: 2.9990 chunk 31 optimal weight: 0.0040 chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 overall best weight: 0.2826 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.145010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120916 restraints weight = 8570.652| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.01 r_work: 0.3278 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 7303 Z= 0.101 Angle : 0.572 14.133 9921 Z= 0.270 Chirality : 0.040 0.142 1182 Planarity : 0.004 0.054 1245 Dihedral : 9.799 72.254 1167 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.34 % Allowed : 18.92 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.28), residues: 946 helix: 1.29 (0.23), residues: 540 sheet: -0.56 (1.17), residues: 24 loop : -1.84 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 44 HIS 0.002 0.001 HIS E 38 PHE 0.014 0.001 PHE C 191 TYR 0.006 0.001 TYR C 248 ARG 0.004 0.000 ARG C 344 Details of bonding type rmsd hydrogen bonds : bond 0.02610 ( 304) hydrogen bonds : angle 3.19030 ( 912) covalent geometry : bond 0.00244 ( 7303) covalent geometry : angle 0.57247 ( 9921) *********************** 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 115 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: C 93 ASP cc_start: 0.8237 (p0) cc_final: 0.7611 (p0) REVERT: C 102 LYS cc_start: 0.9142 (ttpp) cc_final: 0.8864 (ttpt) REVERT: C 132 GLU cc_start: 0.7731 (tt0) cc_final: 0.7171 (pt0) REVERT: C 344 ARG cc_start: 0.8746 (mmm160) cc_final: 0.8420 (mmm160) REVERT: C 387 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7024 (tm-30) REVERT: C 422 LEU cc_start: 0.8324 (mm) cc_final: 0.8105 (mp) REVERT: C 473 ARG cc_start: 0.7496 (ptt-90) cc_final: 0.6984 (ptt-90) REVERT: E 67 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.6978 (tpm-80) REVERT: E 161 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7693 (mm-30) REVERT: D 131 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8052 (mmtt) REVERT: D 171 GLU cc_start: 0.8475 (tp30) cc_final: 0.7876 (tt0) outliers start: 24 outliers final: 12 residues processed: 103 average time/residue: 1.2799 time to fit residues: 138.7239 Evaluate side-chains 104 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 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 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 92 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 57 optimal weight: 0.9980 chunk 43 optimal weight: 0.0870 chunk 6 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 GLN C 409 HIS E 193 HIS D 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114284 restraints weight = 8534.213| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.04 r_work: 0.3205 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7303 Z= 0.141 Angle : 0.596 13.067 9921 Z= 0.287 Chirality : 0.042 0.141 1182 Planarity : 0.005 0.057 1245 Dihedral : 9.713 71.762 1167 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.76 % Allowed : 19.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.27), residues: 946 helix: 1.16 (0.23), residues: 544 sheet: -0.86 (1.13), residues: 24 loop : -1.89 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 44 HIS 0.003 0.001 HIS C 404 PHE 0.017 0.001 PHE C 191 TYR 0.007 0.001 TYR C 248 ARG 0.003 0.000 ARG C 344 Details of bonding type rmsd hydrogen bonds : bond 0.02931 ( 304) hydrogen bonds : angle 3.33230 ( 912) covalent geometry : bond 0.00347 ( 7303) covalent geometry : angle 0.59607 ( 9921) *********************** 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: 27 poor density : 95 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: C 19 ARG cc_start: 0.7290 (ptp90) cc_final: 0.6487 (pmt170) REVERT: C 93 ASP cc_start: 0.8215 (p0) cc_final: 0.7572 (p0) REVERT: C 132 GLU cc_start: 0.7719 (tt0) cc_final: 0.7222 (pt0) REVERT: C 283 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8114 (tp) REVERT: C 344 ARG cc_start: 0.8773 (mmm160) cc_final: 0.8360 (mmm160) REVERT: C 357 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7841 (mp0) REVERT: C 422 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8138 (mp) REVERT: C 473 ARG cc_start: 0.7683 (ptt-90) cc_final: 0.7145 (ptt-90) REVERT: E 67 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.6911 (tpm-80) REVERT: E 161 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7712 (mm-30) REVERT: D 131 LYS cc_start: 0.8864 (mtmt) cc_final: 0.8074 (mmtt) REVERT: D 171 GLU cc_start: 0.8537 (tp30) cc_final: 0.7927 (tt0) REVERT: D 209 ARG cc_start: 0.6955 (ttm170) cc_final: 0.5645 (mmp80) outliers start: 27 outliers final: 15 residues processed: 111 average time/residue: 1.3031 time to fit residues: 152.2704 Evaluate side-chains 113 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 283 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 422 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 92 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 45 optimal weight: 0.0570 chunk 72 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 HIS E 193 HIS D 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.137878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.113723 restraints weight = 8675.016| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.02 r_work: 0.3202 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3129 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= 0.134 Angle : 0.591 11.829 9921 Z= 0.283 Chirality : 0.041 0.142 1182 Planarity : 0.004 0.054 1245 Dihedral : 9.538 71.132 1167 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.48 % Allowed : 19.47 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.27), residues: 946 helix: 1.15 (0.23), residues: 544 sheet: -1.09 (1.09), residues: 24 loop : -1.90 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 44 HIS 0.002 0.001 HIS C 121 PHE 0.015 0.001 PHE C 191 TYR 0.008 0.001 TYR C 248 ARG 0.003 0.000 ARG C 344 Details of bonding type rmsd hydrogen bonds : bond 0.02857 ( 304) hydrogen bonds : angle 3.34568 ( 912) covalent geometry : bond 0.00330 ( 7303) covalent geometry : angle 0.59055 ( 9921) *********************** 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 121 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: C 19 ARG cc_start: 0.7264 (ptp90) cc_final: 0.6486 (pmt170) REVERT: C 67 ARG cc_start: 0.7346 (ttt90) cc_final: 0.7100 (ttt180) REVERT: C 93 ASP cc_start: 0.8216 (p0) cc_final: 0.7546 (p0) REVERT: C 132 GLU cc_start: 0.7650 (tt0) cc_final: 0.7153 (pt0) REVERT: C 344 ARG cc_start: 0.8740 (mmm160) cc_final: 0.8264 (mmm160) REVERT: C 357 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7833 (mp0) REVERT: C 422 LEU cc_start: 0.8390 (mm) cc_final: 0.8161 (mp) REVERT: C 473 ARG cc_start: 0.7704 (ptt-90) cc_final: 0.7390 (ptt-90) REVERT: E 161 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7749 (mm-30) REVERT: D 131 LYS cc_start: 0.8918 (mtmt) cc_final: 0.8136 (mmtt) REVERT: D 171 GLU cc_start: 0.8596 (tp30) cc_final: 0.7995 (tt0) outliers start: 25 outliers final: 15 residues processed: 112 average time/residue: 1.2243 time to fit residues: 144.9539 Evaluate side-chains 110 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 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 512 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 92 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 84 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 0.0070 chunk 27 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.137163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113022 restraints weight = 8619.168| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.01 r_work: 0.3186 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7303 Z= 0.143 Angle : 0.592 10.708 9921 Z= 0.287 Chirality : 0.042 0.145 1182 Planarity : 0.005 0.082 1245 Dihedral : 9.509 71.000 1167 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.34 % Allowed : 19.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.27), residues: 946 helix: 1.13 (0.23), residues: 544 sheet: -1.20 (0.90), residues: 34 loop : -1.95 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 44 HIS 0.002 0.001 HIS C 121 PHE 0.016 0.001 PHE C 191 TYR 0.008 0.001 TYR C 248 ARG 0.004 0.000 ARG D 33 Details of bonding type rmsd hydrogen bonds : bond 0.02920 ( 304) hydrogen bonds : angle 3.37271 ( 912) covalent geometry : bond 0.00351 ( 7303) covalent geometry : angle 0.59243 ( 9921) *********************** 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 123 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 19 ARG cc_start: 0.7275 (ptp90) cc_final: 0.6478 (pmt170) REVERT: C 67 ARG cc_start: 0.7369 (ttt90) cc_final: 0.7107 (ttt180) REVERT: C 93 ASP cc_start: 0.8217 (p0) cc_final: 0.7540 (p0) REVERT: C 344 ARG cc_start: 0.8739 (mmm160) cc_final: 0.8226 (mmm160) REVERT: C 422 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8171 (mp) REVERT: C 473 ARG cc_start: 0.7707 (ptt-90) cc_final: 0.7411 (ptt-90) REVERT: E 67 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.6795 (tpm-80) REVERT: E 161 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7789 (mm-30) REVERT: D 131 LYS cc_start: 0.8921 (mtmt) cc_final: 0.8136 (mmtt) REVERT: D 171 GLU cc_start: 0.8606 (tp30) cc_final: 0.7983 (tt0) REVERT: D 209 ARG cc_start: 0.7147 (ttm170) cc_final: 0.5962 (mmp80) outliers start: 24 outliers final: 18 residues processed: 116 average time/residue: 1.3677 time to fit residues: 166.3727 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 : 0.719 ------------------------------------------------------------------------------- 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 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 422 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 92 THR 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 32 VAL Chi-restraints excluded: chain D residue 105 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 26 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 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 = 0.3589 r_free = 0.3589 target = 0.135702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.111469 restraints weight = 8832.467| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.04 r_work: 0.3164 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3242 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= 0.161 Angle : 0.615 11.109 9921 Z= 0.300 Chirality : 0.043 0.153 1182 Planarity : 0.005 0.087 1245 Dihedral : 9.550 72.657 1167 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.20 % Allowed : 20.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.27), residues: 946 helix: 1.02 (0.23), residues: 544 sheet: -1.44 (0.87), residues: 34 loop : -1.90 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 44 HIS 0.003 0.001 HIS C 404 PHE 0.017 0.001 PHE C 191 TYR 0.009 0.001 TYR C 248 ARG 0.006 0.000 ARG D 33 Details of bonding type rmsd hydrogen bonds : bond 0.03060 ( 304) hydrogen bonds : angle 3.44801 ( 912) covalent geometry : bond 0.00397 ( 7303) covalent geometry : angle 0.61471 ( 9921) ********************** 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 117 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: C 19 ARG cc_start: 0.7248 (ptp90) cc_final: 0.6424 (pmt170) REVERT: C 93 ASP cc_start: 0.8226 (p0) cc_final: 0.7590 (p0) REVERT: C 344 ARG cc_start: 0.8734 (mmm160) cc_final: 0.8207 (mmm160) REVERT: C 473 ARG cc_start: 0.7728 (ptt-90) cc_final: 0.7450 (ptt-90) REVERT: E 161 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7819 (mm-30) REVERT: D 131 LYS cc_start: 0.8928 (mtmt) cc_final: 0.8123 (mmtt) REVERT: D 171 GLU cc_start: 0.8617 (tp30) cc_final: 0.8009 (tt0) outliers start: 23 outliers final: 18 residues processed: 110 average time/residue: 1.2772 time to fit residues: 148.0818 Evaluate side-chains 114 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 311 SER 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 25 LEU Chi-restraints excluded: chain E residue 92 THR 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 32 VAL Chi-restraints excluded: chain D residue 105 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 63 optimal weight: 0.9980 chunk 80 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 83 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.137823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112562 restraints weight = 8573.728| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.06 r_work: 0.3172 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3311 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= 0.136 Angle : 0.588 10.634 9921 Z= 0.287 Chirality : 0.042 0.144 1182 Planarity : 0.004 0.055 1245 Dihedral : 9.366 76.994 1167 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.62 % Allowed : 20.45 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.27), residues: 946 helix: 1.13 (0.23), residues: 544 sheet: -1.65 (0.85), residues: 34 loop : -1.86 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 44 HIS 0.002 0.001 HIS C 121 PHE 0.015 0.001 PHE C 191 TYR 0.008 0.001 TYR C 248 ARG 0.004 0.000 ARG D 33 Details of bonding type rmsd hydrogen bonds : bond 0.02894 ( 304) hydrogen bonds : angle 3.38191 ( 912) covalent geometry : bond 0.00334 ( 7303) covalent geometry : angle 0.58824 ( 9921) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5019.66 seconds wall clock time: 87 minutes 33.67 seconds (5253.67 seconds total)