Starting phenix.real_space_refine on Sat Dec 28 00:35:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1n_36796/12_2024/8k1n_36796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1n_36796/12_2024/8k1n_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_36796/12_2024/8k1n_36796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1n_36796/12_2024/8k1n_36796.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1n_36796/12_2024/8k1n_36796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1n_36796/12_2024/8k1n_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.21, per 1000 atoms: 0.87 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: 2.22 Conformation dependent library (CDL) restraints added in 921.8 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: 0.63 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: 1.78 Time building geometry restraints manager: 2.45 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: 2.330 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.580 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.430 ------------------------------------------------------------------------------- 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= 0.549 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 *********************** 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 : 0.707 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: 1.4154 time to fit residues: 221.1763 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 : 0.754 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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= 0.199 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 *********************** 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 : 0.777 Fit side-chains REVERT: C 93 ASP cc_start: 0.7954 (p0) cc_final: 0.7344 (p0) REVERT: C 412 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7721 (mpp) REVERT: C 488 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.7915 (tp) REVERT: E 30 LEU cc_start: 0.8178 (mp) cc_final: 0.7953 (mm) REVERT: E 161 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7279 (mm-30) REVERT: D 128 ASP cc_start: 0.7457 (t0) cc_final: 0.7064 (t70) REVERT: D 131 LYS cc_start: 0.8318 (mtmt) cc_final: 0.7578 (mmtt) REVERT: D 171 GLU cc_start: 0.7879 (tp30) cc_final: 0.7282 (tt0) REVERT: D 209 ARG cc_start: 0.6510 (ttm170) cc_final: 0.6051 (tpm170) REVERT: D 212 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7586 (mttp) outliers start: 25 outliers final: 8 residues processed: 116 average time/residue: 1.5155 time to fit residues: 184.3301 Evaluate side-chains 103 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 412 MET 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 Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 HIS D 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7303 Z= 0.287 Angle : 0.702 14.829 9921 Z= 0.333 Chirality : 0.044 0.167 1182 Planarity : 0.005 0.059 1245 Dihedral : 11.925 104.961 1167 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.31 % Allowed : 15.44 % Favored : 80.25 % 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: -0.97 (0.26), residues: 946 helix: 0.37 (0.22), residues: 545 sheet: -0.49 (1.17), residues: 24 loop : -2.20 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 44 HIS 0.005 0.001 HIS E 18 PHE 0.018 0.002 PHE C 191 TYR 0.004 0.001 TYR D 86 ARG 0.017 0.001 ARG C 344 *********************** 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 127 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.785 Fit side-chains REVERT: C 93 ASP cc_start: 0.7948 (p0) cc_final: 0.7317 (p0) REVERT: C 125 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7388 (t70) REVERT: C 387 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7373 (tt0) REVERT: C 488 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7915 (tp) REVERT: E 123 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7169 (tm-30) REVERT: E 161 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7423 (mm-30) REVERT: D 34 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6912 (mt-10) REVERT: D 131 LYS cc_start: 0.8696 (mtmt) cc_final: 0.7906 (mmtt) REVERT: D 171 GLU cc_start: 0.8052 (tp30) cc_final: 0.7448 (tt0) REVERT: D 183 GLN cc_start: 0.7655 (pt0) cc_final: 0.7406 (mt0) REVERT: D 209 ARG cc_start: 0.6526 (ttm170) cc_final: 0.5970 (tpm170) outliers start: 31 outliers final: 9 residues processed: 111 average time/residue: 1.4915 time to fit residues: 173.5911 Evaluate side-chains 110 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 123 GLU 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 34 GLU Chi-restraints excluded: chain D residue 105 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.9990 chunk 64 optimal weight: 0.1980 chunk 44 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2668 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= 0.230 Angle : 0.635 14.453 9921 Z= 0.300 Chirality : 0.042 0.148 1182 Planarity : 0.005 0.056 1245 Dihedral : 11.297 102.750 1167 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.59 % Allowed : 16.41 % 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 (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: -0.75 (0.27), residues: 946 helix: 0.59 (0.23), residues: 547 sheet: -1.24 (0.91), residues: 34 loop : -2.13 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 44 HIS 0.003 0.001 HIS C 404 PHE 0.015 0.001 PHE C 191 TYR 0.004 0.001 TYR C 322 ARG 0.010 0.000 ARG C 344 *********************** 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 133 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.810 Fit side-chains REVERT: C 93 ASP cc_start: 0.7978 (p0) cc_final: 0.7378 (p0) REVERT: C 387 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7195 (tt0) REVERT: C 473 ARG cc_start: 0.7629 (ptt-90) cc_final: 0.7205 (ptt-90) REVERT: C 488 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8270 (tt) REVERT: E 13 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6997 (mtt-85) REVERT: E 67 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.6486 (tpm-80) REVERT: E 161 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7482 (mm-30) REVERT: D 131 LYS cc_start: 0.8726 (mtmt) cc_final: 0.7915 (mmtt) REVERT: D 171 GLU cc_start: 0.8044 (tp30) cc_final: 0.7436 (tt0) outliers start: 33 outliers final: 11 residues processed: 119 average time/residue: 1.5676 time to fit residues: 195.3112 Evaluate side-chains 106 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 387 GLU 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 13 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 216 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.5980 chunk 52 optimal weight: 0.0020 chunk 1 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 23 optimal weight: 0.0040 overall best weight: 0.4400 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2849 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= 0.190 Angle : 0.599 14.072 9921 Z= 0.283 Chirality : 0.040 0.137 1182 Planarity : 0.004 0.056 1245 Dihedral : 10.698 91.489 1167 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 5.01 % Allowed : 17.11 % 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: -0.40 (0.27), residues: 946 helix: 0.92 (0.23), residues: 539 sheet: -1.21 (0.92), residues: 34 loop : -2.00 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 44 HIS 0.003 0.001 HIS E 38 PHE 0.014 0.001 PHE C 191 TYR 0.003 0.001 TYR C 91 ARG 0.015 0.000 ARG C 344 *********************** 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 132 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.780 Fit side-chains REVERT: C 19 ARG cc_start: 0.6964 (ptp90) cc_final: 0.6480 (pmt170) REVERT: C 93 ASP cc_start: 0.7974 (p0) cc_final: 0.7306 (p0) REVERT: C 102 LYS cc_start: 0.8722 (ttpp) cc_final: 0.8500 (ttpp) REVERT: C 125 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7251 (t70) REVERT: C 252 ARG cc_start: 0.8356 (mtm180) cc_final: 0.7842 (mtm180) REVERT: C 473 ARG cc_start: 0.7530 (ptt-90) cc_final: 0.7127 (ptt-90) REVERT: C 488 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8092 (tt) REVERT: E 67 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.6391 (tpm-80) REVERT: E 161 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7443 (mm-30) REVERT: D 13 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7479 (mtp85) REVERT: D 131 LYS cc_start: 0.8722 (mtmt) cc_final: 0.7900 (mmtt) REVERT: D 171 GLU cc_start: 0.8032 (tp30) cc_final: 0.7451 (tt0) outliers start: 36 outliers final: 16 residues processed: 120 average time/residue: 1.4757 time to fit residues: 185.7407 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 : 0.834 ------------------------------------------------------------------------------- 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 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 67 ARG Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 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 D 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2965 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= 0.265 Angle : 0.626 13.998 9921 Z= 0.299 Chirality : 0.042 0.147 1182 Planarity : 0.005 0.057 1245 Dihedral : 10.469 82.896 1167 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.31 % Allowed : 19.33 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.49 (0.27), residues: 946 helix: 0.80 (0.23), residues: 546 sheet: -1.27 (0.91), residues: 34 loop : -2.00 (0.29), residues: 366 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 0.004 0.001 TYR D 86 ARG 0.011 0.000 ARG C 344 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: C 19 ARG cc_start: 0.6986 (ptp90) cc_final: 0.6460 (pmt170) REVERT: C 93 ASP cc_start: 0.7937 (p0) cc_final: 0.7300 (p0) REVERT: C 102 LYS cc_start: 0.8727 (ttpp) cc_final: 0.8440 (ttpt) REVERT: C 125 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7383 (t70) REVERT: C 473 ARG cc_start: 0.7536 (ptt-90) cc_final: 0.7316 (ptt-90) REVERT: C 488 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8189 (tt) REVERT: E 67 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.6512 (tpm-80) REVERT: E 161 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7438 (mm-30) REVERT: D 131 LYS cc_start: 0.8713 (mtmt) cc_final: 0.7888 (mmtt) REVERT: D 171 GLU cc_start: 0.8099 (tp30) cc_final: 0.7558 (tt0) outliers start: 31 outliers final: 17 residues processed: 113 average time/residue: 1.5471 time to fit residues: 184.0249 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 : 0.979 ------------------------------------------------------------------------------- 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 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 67 ARG 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 Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.0170 chunk 52 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 0.0070 overall best weight: 0.4236 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3095 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= 0.188 Angle : 0.585 13.499 9921 Z= 0.281 Chirality : 0.040 0.136 1182 Planarity : 0.005 0.055 1245 Dihedral : 10.031 75.803 1167 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.76 % Allowed : 20.31 % 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: -0.19 (0.27), residues: 946 helix: 1.10 (0.23), residues: 539 sheet: -1.46 (0.88), residues: 34 loop : -1.89 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 44 HIS 0.003 0.001 HIS E 38 PHE 0.013 0.001 PHE C 191 TYR 0.003 0.001 TYR C 91 ARG 0.012 0.000 ARG C 344 *********************** 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 123 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.796 Fit side-chains REVERT: C 19 ARG cc_start: 0.6977 (ptp90) cc_final: 0.6474 (pmt170) REVERT: C 93 ASP cc_start: 0.7921 (p0) cc_final: 0.7306 (p0) REVERT: C 102 LYS cc_start: 0.8702 (ttpp) cc_final: 0.8482 (ttpp) REVERT: C 252 ARG cc_start: 0.8358 (mtm180) cc_final: 0.7808 (mtm180) REVERT: C 387 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7139 (tt0) REVERT: C 473 ARG cc_start: 0.7459 (ptt-90) cc_final: 0.7196 (ptt-90) REVERT: E 13 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6839 (mtt-85) REVERT: E 67 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6490 (tpm-80) REVERT: E 161 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7427 (mm-30) REVERT: D 131 LYS cc_start: 0.8667 (mtmt) cc_final: 0.7859 (mmtt) REVERT: D 171 GLU cc_start: 0.8094 (tp30) cc_final: 0.7534 (tt0) outliers start: 27 outliers final: 16 residues processed: 113 average time/residue: 1.4361 time to fit residues: 170.2893 Evaluate side-chains 114 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 325 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain E residue 13 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 212 LYS Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.0000 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 80 optimal weight: 1.9990 overall best weight: 0.3384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3248 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= 0.173 Angle : 0.587 12.328 9921 Z= 0.279 Chirality : 0.040 0.131 1182 Planarity : 0.005 0.056 1245 Dihedral : 9.595 71.538 1167 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.48 % Allowed : 21.00 % Favored : 75.52 % 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 (0.27), residues: 946 helix: 1.23 (0.23), residues: 538 sheet: -1.56 (0.88), residues: 34 loop : -1.81 (0.30), residues: 374 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 0.008 0.001 TYR C 489 ARG 0.015 0.000 ARG C 344 *********************** 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 122 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: C 19 ARG cc_start: 0.6962 (ptp90) cc_final: 0.6446 (pmt170) REVERT: C 67 ARG cc_start: 0.7298 (ttt90) cc_final: 0.7051 (tpt170) REVERT: C 93 ASP cc_start: 0.7983 (p0) cc_final: 0.7305 (p0) REVERT: C 252 ARG cc_start: 0.8337 (mtm180) cc_final: 0.7825 (mtm180) REVERT: C 387 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: C 473 ARG cc_start: 0.7408 (ptt-90) cc_final: 0.7159 (ptt-90) REVERT: E 13 ARG cc_start: 0.7119 (ptp-110) cc_final: 0.6855 (mmt180) REVERT: E 161 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7469 (mm-30) REVERT: D 131 LYS cc_start: 0.8657 (mtmt) cc_final: 0.7835 (mmtt) REVERT: D 138 LYS cc_start: 0.8902 (ttpp) cc_final: 0.8697 (ttpt) REVERT: D 171 GLU cc_start: 0.8085 (tp30) cc_final: 0.7520 (tt0) outliers start: 25 outliers final: 17 residues processed: 114 average time/residue: 1.4083 time to fit residues: 168.9031 Evaluate side-chains 111 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 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 Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 0.0470 chunk 67 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 0.0470 chunk 80 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 overall best weight: 0.3976 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3305 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= 0.184 Angle : 0.572 10.920 9921 Z= 0.275 Chirality : 0.040 0.133 1182 Planarity : 0.005 0.062 1245 Dihedral : 9.452 70.696 1167 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.92 % Allowed : 21.56 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.28), residues: 946 helix: 1.23 (0.23), residues: 541 sheet: -1.56 (0.88), residues: 34 loop : -1.77 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 44 HIS 0.003 0.001 HIS E 38 PHE 0.014 0.001 PHE C 191 TYR 0.004 0.001 TYR C 91 ARG 0.015 0.000 ARG C 344 *********************** 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 116 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: C 19 ARG cc_start: 0.6953 (ptp90) cc_final: 0.6444 (pmt170) REVERT: C 67 ARG cc_start: 0.7317 (ttt90) cc_final: 0.7106 (tpt170) REVERT: C 93 ASP cc_start: 0.7970 (p0) cc_final: 0.7325 (p0) REVERT: C 252 ARG cc_start: 0.8306 (mtm180) cc_final: 0.7796 (mtm180) REVERT: C 387 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: C 473 ARG cc_start: 0.7460 (ptt-90) cc_final: 0.7099 (ptt-90) REVERT: E 67 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.6610 (tpm-80) REVERT: E 161 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7440 (mm-30) REVERT: D 131 LYS cc_start: 0.8649 (mtmt) cc_final: 0.7819 (mmtt) REVERT: D 138 LYS cc_start: 0.8903 (ttpp) cc_final: 0.8692 (ttpt) REVERT: D 171 GLU cc_start: 0.8079 (tp30) cc_final: 0.7527 (tt0) outliers start: 21 outliers final: 17 residues processed: 107 average time/residue: 1.4899 time to fit residues: 167.2766 Evaluate side-chains 114 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 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 Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 87 optimal weight: 0.3980 chunk 75 optimal weight: 0.1980 chunk 7 optimal weight: 0.0970 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 80 optimal weight: 0.0670 chunk 23 optimal weight: 0.8980 overall best weight: 0.3116 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3374 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= 0.171 Angle : 0.567 11.016 9921 Z= 0.271 Chirality : 0.040 0.152 1182 Planarity : 0.005 0.064 1245 Dihedral : 9.276 71.250 1167 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.92 % Allowed : 21.42 % Favored : 75.66 % 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: 1.30 (0.23), residues: 540 sheet: -1.58 (0.89), residues: 34 loop : -1.75 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 44 HIS 0.003 0.001 HIS E 38 PHE 0.013 0.001 PHE C 191 TYR 0.004 0.001 TYR C 91 ARG 0.015 0.000 ARG C 344 ********************** 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 116 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: C 19 ARG cc_start: 0.6945 (ptp90) cc_final: 0.6458 (pmt170) REVERT: C 93 ASP cc_start: 0.7994 (p0) cc_final: 0.7356 (p0) REVERT: C 252 ARG cc_start: 0.8282 (mtm180) cc_final: 0.7766 (mtm180) REVERT: C 387 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: C 473 ARG cc_start: 0.7409 (ptt-90) cc_final: 0.7074 (ptt-90) REVERT: E 13 ARG cc_start: 0.7576 (mmt180) cc_final: 0.7255 (mmt180) REVERT: E 67 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6658 (tpm-80) REVERT: E 161 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7496 (mm-30) REVERT: D 131 LYS cc_start: 0.8656 (mtmt) cc_final: 0.7808 (mmtt) REVERT: D 138 LYS cc_start: 0.8900 (ttpp) cc_final: 0.8694 (ttpt) REVERT: D 171 GLU cc_start: 0.8024 (tp30) cc_final: 0.7482 (tt0) outliers start: 21 outliers final: 16 residues processed: 108 average time/residue: 1.5276 time to fit residues: 172.8461 Evaluate side-chains 112 residues out of total 719 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 356 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 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 Chi-restraints excluded: chain D residue 212 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 75 optimal weight: 0.3980 chunk 31 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3606 r_free = 0.3606 target = 0.137043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.112813 restraints weight = 8493.845| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.00 r_work: 0.3197 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3345 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= 0.228 Angle : 0.581 10.548 9921 Z= 0.283 Chirality : 0.041 0.151 1182 Planarity : 0.005 0.062 1245 Dihedral : 9.286 72.771 1167 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.20 % Allowed : 21.00 % 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 (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: 1.15 (0.23), residues: 544 sheet: -1.69 (0.87), residues: 34 loop : -1.82 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 44 HIS 0.003 0.001 HIS E 38 PHE 0.016 0.001 PHE C 191 TYR 0.004 0.001 TYR C 64 ARG 0.014 0.000 ARG C 344 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3354.16 seconds wall clock time: 61 minutes 44.50 seconds (3704.50 seconds total)