Starting phenix.real_space_refine on Wed Mar 12 15:28:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k0j_22599/03_2025/7k0j_22599.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0j_22599/03_2025/7k0j_22599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k0j_22599/03_2025/7k0j_22599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0j_22599/03_2025/7k0j_22599.map" model { file = "/net/cci-nas-00/data/ceres_data/7k0j_22599/03_2025/7k0j_22599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0j_22599/03_2025/7k0j_22599.cif" } resolution = 3.1 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= -0.002 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 44 5.16 5 C 4920 2.51 5 N 1305 2.21 5 O 1413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7683 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3287 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 5.72, per 1000 atoms: 0.74 Number of scatterers: 7683 At special positions: 0 Unit cell: (88.044, 81.0405, 128.064, 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 44 16.00 P 1 15.00 O 1413 8.00 N 1305 7.00 C 4920 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 844.8 milliseconds 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1804 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 51.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.673A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 179 removed outlier: 4.536A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 213 through 231 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 359 removed outlier: 3.694A pdb=" N ASN A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 377 removed outlier: 4.070A pdb=" N ALA A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 422 removed outlier: 3.615A pdb=" N ARG A 422 " --> pdb=" O GLN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 472 Processing helix chain 'B' and resid 67 through 94 Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.588A pdb=" N LYS B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 126 removed outlier: 3.784A pdb=" N ASN B 120 " --> pdb=" O GLN B 116 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TYR B 122 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N THR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 134 removed outlier: 5.684A pdb=" N ASP B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.621A pdb=" N GLU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 Proline residue: B 247 - end of helix removed outlier: 3.559A pdb=" N VAL B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 273 Processing helix chain 'B' and resid 284 through 298 Processing helix chain 'B' and resid 326 through 337 Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 433 through 455 removed outlier: 3.576A pdb=" N GLU B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.901A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG B 489 " --> pdb=" O GLU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 30 through 55 Processing helix chain 'C' and resid 58 through 69 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95 removed outlier: 6.883A pdb=" N ALA A 425 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164 removed outlier: 7.052A pdb=" N ILE A 271 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N SER A 304 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 273 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARG A 240 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N PHE A 272 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE A 242 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLU A 274 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A 244 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 386 removed outlier: 4.069A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 153 removed outlier: 6.734A pdb=" N VAL B 146 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE B 167 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE B 148 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ASN B 165 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU B 150 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.644A pdb=" N ILE B 310 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP B 259 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N GLU B 315 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.860A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1122 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: 2.12 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: 1.22 - 1.34: 2500 1.34 - 1.46: 1123 1.46 - 1.57: 4144 1.57 - 1.69: 1 1.69 - 1.81: 71 Bond restraints: 7839 Sorted by residual: bond pdb=" N PHE B 121 " pdb=" CA PHE B 121 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.16e-02 7.43e+03 7.12e+00 bond pdb=" N ASN B 120 " pdb=" CA ASN B 120 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.21e+00 bond pdb=" N GLU B 119 " pdb=" CA GLU B 119 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.21e-02 6.83e+03 5.91e+00 bond pdb=" N PHE B 118 " pdb=" CA PHE B 118 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.25e-02 6.40e+03 5.80e+00 bond pdb=" C ARG A 287 " pdb=" N GLY A 288 " ideal model delta sigma weight residual 1.334 1.318 0.016 1.12e-02 7.97e+03 1.95e+00 ... (remaining 7834 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 10377 2.06 - 4.11: 190 4.11 - 6.17: 20 6.17 - 8.23: 2 8.23 - 10.28: 2 Bond angle restraints: 10591 Sorted by residual: angle pdb=" C GLY B 497 " pdb=" N PHE B 498 " pdb=" CA PHE B 498 " ideal model delta sigma weight residual 120.09 125.22 -5.13 1.25e+00 6.40e-01 1.68e+01 angle pdb=" C VAL A 130 " pdb=" N GLY A 131 " pdb=" CA GLY A 131 " ideal model delta sigma weight residual 122.18 119.85 2.33 6.90e-01 2.10e+00 1.14e+01 angle pdb=" C LEU B 365 " pdb=" N ASP B 366 " pdb=" CA ASP B 366 " ideal model delta sigma weight residual 121.59 131.87 -10.28 3.54e+00 7.98e-02 8.44e+00 angle pdb=" CA PHE B 121 " pdb=" C PHE B 121 " pdb=" O PHE B 121 " ideal model delta sigma weight residual 121.07 117.93 3.14 1.10e+00 8.26e-01 8.17e+00 angle pdb=" C ILE B 426 " pdb=" N MET B 427 " pdb=" CA MET B 427 " ideal model delta sigma weight residual 122.65 118.00 4.65 1.66e+00 3.63e-01 7.83e+00 ... (remaining 10586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4320 17.92 - 35.85: 329 35.85 - 53.77: 56 53.77 - 71.69: 5 71.69 - 89.62: 7 Dihedral angle restraints: 4717 sinusoidal: 1894 harmonic: 2823 Sorted by residual: dihedral pdb=" CA TYR B 461 " pdb=" C TYR B 461 " pdb=" N GLY B 462 " pdb=" CA GLY B 462 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA MET C 28 " pdb=" C MET C 28 " pdb=" N LEU C 29 " pdb=" CA LEU C 29 " ideal model delta harmonic sigma weight residual -180.00 -163.55 -16.45 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB GLU A 451 " pdb=" CG GLU A 451 " pdb=" CD GLU A 451 " pdb=" OE1 GLU A 451 " ideal model delta sinusoidal sigma weight residual 0.00 89.62 -89.62 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 4714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 705 0.036 - 0.071: 320 0.071 - 0.107: 108 0.107 - 0.143: 35 0.143 - 0.178: 1 Chirality restraints: 1169 Sorted by residual: chirality pdb=" CB ILE B 388 " pdb=" CA ILE B 388 " pdb=" CG1 ILE B 388 " pdb=" CG2 ILE B 388 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" CA LEU A 257 " pdb=" N LEU A 257 " pdb=" C LEU A 257 " pdb=" CB LEU A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE A 242 " pdb=" N ILE A 242 " pdb=" C ILE A 242 " pdb=" CB ILE A 242 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1166 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 166 " 0.016 2.00e-02 2.50e+03 1.20e-02 2.88e+00 pdb=" CG TYR A 166 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 166 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 166 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 166 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 166 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 166 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 166 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 469 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO B 470 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 498 " 0.028 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO B 499 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 499 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 499 " 0.024 5.00e-02 4.00e+02 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1091 2.75 - 3.29: 7066 3.29 - 3.82: 12146 3.82 - 4.36: 14558 4.36 - 4.90: 26836 Nonbonded interactions: 61697 Sorted by model distance: nonbonded pdb=" OD2 ASP A 228 " pdb=" NH2 ARG A 240 " model vdw 2.210 3.120 nonbonded pdb=" OE2 GLU A 274 " pdb=" OG SER A 276 " model vdw 2.221 3.040 nonbonded pdb=" O GLU A 67 " pdb=" OH TYR B 340 " model vdw 2.282 3.040 nonbonded pdb=" OG1 THR B 378 " pdb=" O3P PLP B 601 " model vdw 2.282 3.040 nonbonded pdb=" NH2 ARG A 270 " pdb=" OE2 GLU B 104 " model vdw 2.314 3.120 ... (remaining 61692 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.820 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.070 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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 : 0.006 0.043 7839 Z= 0.412 Angle : 0.712 10.284 10591 Z= 0.407 Chirality : 0.046 0.178 1169 Planarity : 0.004 0.041 1360 Dihedral : 13.138 89.617 2913 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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 (0.26), residues: 971 helix: 1.30 (0.24), residues: 444 sheet: -0.62 (0.50), residues: 113 loop : -0.92 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 32 HIS 0.004 0.001 HIS B 403 PHE 0.019 0.002 PHE A 168 TYR 0.029 0.002 TYR A 166 ARG 0.004 0.001 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.832 Fit side-chains REVERT: A 132 THR cc_start: 0.8937 (p) cc_final: 0.8703 (p) REVERT: A 227 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6501 (mt-10) REVERT: A 233 ARG cc_start: 0.7536 (mtp-110) cc_final: 0.7269 (mpt180) REVERT: A 331 SER cc_start: 0.8381 (m) cc_final: 0.8162 (m) REVERT: A 434 LYS cc_start: 0.8606 (mppt) cc_final: 0.8160 (mmmt) REVERT: B 95 ARG cc_start: 0.7963 (tpp-160) cc_final: 0.6509 (tpt90) REVERT: B 285 MET cc_start: 0.7729 (mmt) cc_final: 0.7178 (mmt) REVERT: C 40 MET cc_start: 0.6571 (tmm) cc_final: 0.6199 (tmm) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2502 time to fit residues: 28.5177 Evaluate side-chains 76 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.112653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.092997 restraints weight = 9891.270| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.31 r_work: 0.2951 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7839 Z= 0.276 Angle : 0.560 10.508 10591 Z= 0.292 Chirality : 0.043 0.136 1169 Planarity : 0.005 0.040 1360 Dihedral : 5.386 72.686 1092 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.37 % Allowed : 6.58 % Favored : 93.04 % 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: 0.64 (0.27), residues: 971 helix: 1.69 (0.24), residues: 445 sheet: -0.14 (0.48), residues: 125 loop : -0.81 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.005 0.001 HIS B 403 PHE 0.016 0.001 PHE A 209 TYR 0.019 0.001 TYR A 166 ARG 0.003 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.852 Fit side-chains REVERT: A 233 ARG cc_start: 0.7643 (mtp-110) cc_final: 0.7091 (mpt180) REVERT: A 331 SER cc_start: 0.8228 (m) cc_final: 0.7974 (m) REVERT: A 434 LYS cc_start: 0.8803 (mppt) cc_final: 0.8288 (mmmt) REVERT: B 95 ARG cc_start: 0.7838 (tpp-160) cc_final: 0.6441 (tpt170) REVERT: B 161 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7259 (ptmt) REVERT: B 173 MET cc_start: 0.8818 (mtt) cc_final: 0.8384 (mtt) REVERT: B 244 MET cc_start: 0.8745 (mtt) cc_final: 0.8322 (mtt) REVERT: B 285 MET cc_start: 0.7785 (mmt) cc_final: 0.7409 (mmt) REVERT: C 40 MET cc_start: 0.6503 (tmm) cc_final: 0.6164 (tmm) outliers start: 3 outliers final: 3 residues processed: 80 average time/residue: 0.2521 time to fit residues: 26.4307 Evaluate side-chains 78 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.092703 restraints weight = 9925.351| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.46 r_work: 0.2940 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7839 Z= 0.254 Angle : 0.526 9.464 10591 Z= 0.273 Chirality : 0.042 0.127 1169 Planarity : 0.004 0.038 1360 Dihedral : 5.220 72.879 1092 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.87 % Allowed : 8.57 % Favored : 90.56 % 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: 0.80 (0.27), residues: 971 helix: 1.87 (0.25), residues: 445 sheet: -0.08 (0.53), residues: 111 loop : -0.77 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.003 0.001 HIS B 403 PHE 0.014 0.001 PHE A 209 TYR 0.016 0.001 TYR B 539 ARG 0.002 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.925 Fit side-chains REVERT: A 233 ARG cc_start: 0.7611 (mtp-110) cc_final: 0.7067 (mpt180) REVERT: A 331 SER cc_start: 0.8170 (m) cc_final: 0.7918 (m) REVERT: A 434 LYS cc_start: 0.8796 (mppt) cc_final: 0.8266 (mmmt) REVERT: B 95 ARG cc_start: 0.7781 (tpp-160) cc_final: 0.6391 (tpt170) REVERT: B 161 LYS cc_start: 0.8263 (mtmt) cc_final: 0.7305 (ptmt) REVERT: B 285 MET cc_start: 0.7831 (mmt) cc_final: 0.7531 (mmt) outliers start: 7 outliers final: 4 residues processed: 85 average time/residue: 0.2447 time to fit residues: 27.6323 Evaluate side-chains 81 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 83 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.111858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.092007 restraints weight = 9870.617| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.35 r_work: 0.2946 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7839 Z= 0.268 Angle : 0.524 9.094 10591 Z= 0.272 Chirality : 0.042 0.127 1169 Planarity : 0.004 0.038 1360 Dihedral : 5.200 74.542 1092 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.49 % Allowed : 9.32 % Favored : 89.19 % 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: 0.79 (0.27), residues: 971 helix: 1.89 (0.25), residues: 445 sheet: -0.13 (0.52), residues: 111 loop : -0.81 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.003 0.001 HIS B 403 PHE 0.014 0.001 PHE A 209 TYR 0.016 0.001 TYR B 539 ARG 0.002 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.795 Fit side-chains REVERT: A 233 ARG cc_start: 0.7623 (mtp-110) cc_final: 0.7100 (mpt180) REVERT: A 331 SER cc_start: 0.8147 (m) cc_final: 0.7887 (m) REVERT: A 434 LYS cc_start: 0.8798 (mppt) cc_final: 0.8270 (mmmt) REVERT: B 95 ARG cc_start: 0.7781 (tpp-160) cc_final: 0.6461 (tpt170) REVERT: B 161 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7309 (ptmt) REVERT: B 285 MET cc_start: 0.7811 (mmt) cc_final: 0.7564 (mmt) REVERT: C 40 MET cc_start: 0.6527 (tmm) cc_final: 0.6196 (tmm) outliers start: 12 outliers final: 7 residues processed: 83 average time/residue: 0.2959 time to fit residues: 32.5689 Evaluate side-chains 83 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 517 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 44 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.113509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.092565 restraints weight = 9943.501| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.45 r_work: 0.2945 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7839 Z= 0.250 Angle : 0.510 8.847 10591 Z= 0.265 Chirality : 0.042 0.127 1169 Planarity : 0.004 0.038 1360 Dihedral : 5.169 75.922 1092 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.37 % Allowed : 10.06 % Favored : 88.57 % 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: 971 helix: 1.93 (0.25), residues: 446 sheet: -0.39 (0.51), residues: 110 loop : -0.85 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.003 0.001 HIS B 403 PHE 0.014 0.001 PHE A 209 TYR 0.014 0.001 TYR B 539 ARG 0.002 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.864 Fit side-chains REVERT: A 233 ARG cc_start: 0.7609 (mtp-110) cc_final: 0.7085 (mpt180) REVERT: A 331 SER cc_start: 0.8139 (m) cc_final: 0.7879 (m) REVERT: A 434 LYS cc_start: 0.8803 (mppt) cc_final: 0.8276 (mmmt) REVERT: B 95 ARG cc_start: 0.7726 (tpp-160) cc_final: 0.6387 (tpt170) REVERT: B 161 LYS cc_start: 0.8251 (mtmt) cc_final: 0.7302 (ptmt) REVERT: C 40 MET cc_start: 0.6490 (tmm) cc_final: 0.6145 (tmm) outliers start: 11 outliers final: 9 residues processed: 83 average time/residue: 0.2370 time to fit residues: 26.1177 Evaluate side-chains 85 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 388 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 59 optimal weight: 0.0870 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.112839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.093145 restraints weight = 9799.069| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.33 r_work: 0.2964 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7839 Z= 0.217 Angle : 0.489 8.663 10591 Z= 0.254 Chirality : 0.041 0.127 1169 Planarity : 0.004 0.037 1360 Dihedral : 5.109 76.401 1092 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.37 % Allowed : 10.93 % Favored : 87.70 % 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: 0.83 (0.27), residues: 971 helix: 2.03 (0.25), residues: 446 sheet: -0.37 (0.51), residues: 110 loop : -0.84 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.002 0.001 HIS B 403 PHE 0.012 0.001 PHE A 209 TYR 0.011 0.001 TYR B 539 ARG 0.002 0.000 ARG B 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.779 Fit side-chains REVERT: A 150 ASP cc_start: 0.7720 (t0) cc_final: 0.7293 (t0) REVERT: A 233 ARG cc_start: 0.7593 (mtp-110) cc_final: 0.7082 (mpt180) REVERT: A 331 SER cc_start: 0.8123 (m) cc_final: 0.7859 (m) REVERT: A 434 LYS cc_start: 0.8804 (mppt) cc_final: 0.8281 (mmmt) REVERT: B 95 ARG cc_start: 0.7719 (tpp-160) cc_final: 0.6404 (tpt170) REVERT: B 161 LYS cc_start: 0.8271 (mtmt) cc_final: 0.7319 (ptmt) REVERT: C 40 MET cc_start: 0.6494 (tmm) cc_final: 0.6142 (tmm) outliers start: 11 outliers final: 8 residues processed: 92 average time/residue: 0.2336 time to fit residues: 28.4343 Evaluate side-chains 86 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 83 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 50 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.110643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.091049 restraints weight = 9900.427| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.33 r_work: 0.2949 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7839 Z= 0.268 Angle : 0.515 8.526 10591 Z= 0.268 Chirality : 0.042 0.126 1169 Planarity : 0.004 0.037 1360 Dihedral : 5.141 76.675 1092 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.86 % Allowed : 10.68 % Favored : 87.45 % 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: 0.77 (0.27), residues: 971 helix: 1.96 (0.25), residues: 446 sheet: -0.39 (0.51), residues: 110 loop : -0.86 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.003 0.001 HIS B 403 PHE 0.014 0.001 PHE A 209 TYR 0.013 0.001 TYR B 539 ARG 0.003 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.800 Fit side-chains REVERT: A 233 ARG cc_start: 0.7609 (mtp-110) cc_final: 0.7096 (mpt180) REVERT: A 331 SER cc_start: 0.8156 (m) cc_final: 0.7894 (m) REVERT: A 434 LYS cc_start: 0.8812 (mppt) cc_final: 0.8288 (mmmt) REVERT: B 95 ARG cc_start: 0.7729 (tpp-160) cc_final: 0.6410 (tpt170) REVERT: B 161 LYS cc_start: 0.8281 (mtmt) cc_final: 0.7325 (ptmt) REVERT: B 285 MET cc_start: 0.7728 (mmt) cc_final: 0.7418 (mmt) REVERT: C 40 MET cc_start: 0.6527 (tmm) cc_final: 0.6255 (tmm) outliers start: 15 outliers final: 10 residues processed: 89 average time/residue: 0.2239 time to fit residues: 26.7603 Evaluate side-chains 87 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS B 184 ASN B 542 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.112186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.092335 restraints weight = 9947.252| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.35 r_work: 0.2953 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7839 Z= 0.247 Angle : 0.503 8.477 10591 Z= 0.262 Chirality : 0.042 0.126 1169 Planarity : 0.004 0.036 1360 Dihedral : 5.136 77.455 1092 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.61 % Allowed : 11.43 % Favored : 86.96 % 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: 0.80 (0.27), residues: 971 helix: 2.01 (0.25), residues: 445 sheet: -0.37 (0.51), residues: 110 loop : -0.86 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.002 0.001 HIS B 403 PHE 0.013 0.001 PHE A 209 TYR 0.011 0.001 TYR B 448 ARG 0.003 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.776 Fit side-chains REVERT: A 132 THR cc_start: 0.9079 (p) cc_final: 0.8816 (p) REVERT: A 150 ASP cc_start: 0.7673 (t0) cc_final: 0.7338 (t0) REVERT: A 233 ARG cc_start: 0.7575 (mtp-110) cc_final: 0.7069 (mpt180) REVERT: A 331 SER cc_start: 0.8143 (m) cc_final: 0.7870 (m) REVERT: A 434 LYS cc_start: 0.8812 (mppt) cc_final: 0.8283 (mmmt) REVERT: B 95 ARG cc_start: 0.7698 (tpp-160) cc_final: 0.6364 (tpt170) REVERT: B 161 LYS cc_start: 0.8281 (mtmt) cc_final: 0.7316 (ptmt) REVERT: C 40 MET cc_start: 0.6531 (tmm) cc_final: 0.6256 (tmm) outliers start: 13 outliers final: 9 residues processed: 87 average time/residue: 0.2281 time to fit residues: 26.5400 Evaluate side-chains 86 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 91 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 18 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 95 optimal weight: 0.0050 chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 0.0020 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS B 542 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.114602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.094891 restraints weight = 9847.513| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.34 r_work: 0.2989 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7839 Z= 0.161 Angle : 0.457 7.868 10591 Z= 0.240 Chirality : 0.040 0.127 1169 Planarity : 0.004 0.036 1360 Dihedral : 4.997 76.788 1092 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.87 % Allowed : 12.92 % Favored : 86.21 % 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: 1.01 (0.27), residues: 971 helix: 2.16 (0.25), residues: 451 sheet: -0.22 (0.52), residues: 110 loop : -0.77 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.002 0.001 HIS A 77 PHE 0.010 0.001 PHE B 280 TYR 0.007 0.001 TYR B 448 ARG 0.003 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.798 Fit side-chains REVERT: A 150 ASP cc_start: 0.7619 (t0) cc_final: 0.7266 (t0) REVERT: A 233 ARG cc_start: 0.7576 (mtp-110) cc_final: 0.7072 (mtm-85) REVERT: A 331 SER cc_start: 0.8065 (m) cc_final: 0.7812 (m) REVERT: A 434 LYS cc_start: 0.8782 (mppt) cc_final: 0.8249 (mmmt) REVERT: B 95 ARG cc_start: 0.7665 (tpp-160) cc_final: 0.6353 (tpt170) REVERT: B 161 LYS cc_start: 0.8278 (mtmt) cc_final: 0.7318 (ptmt) REVERT: B 285 MET cc_start: 0.7591 (mmt) cc_final: 0.7033 (mmt) REVERT: C 13 MET cc_start: 0.6465 (tpt) cc_final: 0.6258 (mmm) REVERT: C 40 MET cc_start: 0.6581 (tmm) cc_final: 0.6268 (tmm) outliers start: 7 outliers final: 4 residues processed: 86 average time/residue: 0.2416 time to fit residues: 27.3982 Evaluate side-chains 85 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 91 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS B 542 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.112902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.093253 restraints weight = 9877.139| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.34 r_work: 0.2964 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7839 Z= 0.231 Angle : 0.490 8.231 10591 Z= 0.255 Chirality : 0.041 0.127 1169 Planarity : 0.004 0.036 1360 Dihedral : 5.019 76.458 1092 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.87 % Allowed : 13.04 % Favored : 86.09 % 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 (0.27), residues: 971 helix: 2.16 (0.25), residues: 445 sheet: -0.28 (0.52), residues: 110 loop : -0.80 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.003 0.001 HIS A 77 PHE 0.013 0.001 PHE A 209 TYR 0.011 0.001 TYR B 448 ARG 0.003 0.000 ARG A 240 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1942 Ramachandran restraints generated. 971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.941 Fit side-chains REVERT: A 132 THR cc_start: 0.9075 (p) cc_final: 0.8812 (p) REVERT: A 150 ASP cc_start: 0.7655 (t0) cc_final: 0.7300 (t0) REVERT: A 233 ARG cc_start: 0.7581 (mtp-110) cc_final: 0.7169 (mpt180) REVERT: A 331 SER cc_start: 0.8111 (m) cc_final: 0.7848 (m) REVERT: A 434 LYS cc_start: 0.8790 (mppt) cc_final: 0.8256 (mmmt) REVERT: B 95 ARG cc_start: 0.7674 (tpp-160) cc_final: 0.6355 (tpt170) REVERT: B 161 LYS cc_start: 0.8271 (mtmt) cc_final: 0.7373 (ptmt) REVERT: B 285 MET cc_start: 0.7630 (mmt) cc_final: 0.7062 (mmt) REVERT: C 40 MET cc_start: 0.6586 (tmm) cc_final: 0.6281 (tmm) outliers start: 7 outliers final: 7 residues processed: 86 average time/residue: 0.3067 time to fit residues: 35.2019 Evaluate side-chains 86 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 395 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 61 optimal weight: 0.1980 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS B 542 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.113712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.093899 restraints weight = 9847.630| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.35 r_work: 0.2975 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7839 Z= 0.197 Angle : 0.472 8.073 10591 Z= 0.246 Chirality : 0.041 0.127 1169 Planarity : 0.004 0.035 1360 Dihedral : 4.990 76.563 1092 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.12 % Allowed : 12.92 % Favored : 85.96 % 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: 0.99 (0.27), residues: 971 helix: 2.14 (0.25), residues: 450 sheet: -0.25 (0.52), residues: 110 loop : -0.78 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 32 HIS 0.002 0.001 HIS A 77 PHE 0.012 0.001 PHE A 209 TYR 0.010 0.001 TYR B 448 ARG 0.003 0.000 ARG A 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3925.19 seconds wall clock time: 69 minutes 27.63 seconds (4167.63 seconds total)