Starting phenix.real_space_refine on Wed Mar 12 21:32:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rla_19336/03_2025/8rla_19336.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rla_19336/03_2025/8rla_19336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rla_19336/03_2025/8rla_19336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rla_19336/03_2025/8rla_19336.map" model { file = "/net/cci-nas-00/data/ceres_data/8rla_19336/03_2025/8rla_19336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rla_19336/03_2025/8rla_19336.cif" } resolution = 3.03 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= 0.018 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 27 5.16 5 C 2660 2.51 5 N 739 2.21 5 O 786 1.98 5 H 4091 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8304 Number of models: 1 Model: "" Number of chains: 3 Chain: "K" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1816 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6487 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 17, 'TRANS': 418} Chain breaks: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 82 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7746 SG CYS A 411 27.463 58.933 52.409 1.00 93.45 S ATOM 7981 SG CYS A 427 24.261 57.152 53.131 1.00110.96 S ATOM 8030 SG CYS A 431 26.115 59.424 55.841 1.00 94.26 S ATOM 8069 SG CYS A 434 24.072 60.799 52.922 1.00 73.98 S Time building chain proxies: 5.46, per 1000 atoms: 0.66 Number of scatterers: 8304 At special positions: 0 Unit cell: (73.87, 88.81, 96.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 27 16.00 O 786 8.00 N 739 7.00 C 2660 6.00 H 4091 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 95 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 272 " distance=2.03 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: 2.28 Conformation dependent library (CDL) restraints added in 853.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 411 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 434 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 427 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 431 " Number of angles added : 6 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 4 sheets defined 45.2% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'K' and resid 60 through 65 removed outlier: 4.665A pdb=" N GLY K 65 " --> pdb=" O ASP K 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 23 Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 59 through 69 Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 79 through 93 removed outlier: 3.551A pdb=" N LEU A 93 " --> pdb=" O HIS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 170 through 182 removed outlier: 3.748A pdb=" N LEU A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY A 177 " --> pdb=" O TYR A 173 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 207 Processing helix chain 'A' and resid 237 through 251 Processing helix chain 'A' and resid 268 through 283 removed outlier: 3.514A pdb=" N GLN A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 307 Processing helix chain 'A' and resid 339 through 349 removed outlier: 3.807A pdb=" N ARG A 349 " --> pdb=" O GLN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 386 Processing helix chain 'A' and resid 388 through 408 Processing helix chain 'A' and resid 411 through 421 Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 436 through 451 Processing sheet with id=AA1, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.511A pdb=" N LEU K 20 " --> pdb=" O LEU K 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 57 through 58 removed outlier: 6.639A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N MET K 34 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR K 52 " --> pdb=" O ASN K 32 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASN K 32 " --> pdb=" O THR K 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 57 through 58 removed outlier: 6.639A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N MET K 34 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR K 52 " --> pdb=" O ASN K 32 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASN K 32 " --> pdb=" O THR K 52 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N TYR K 101 " --> pdb=" O PHE K 29 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE K 31 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLY K 99 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP A 47 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N PHE A 216 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE A 49 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 48 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N THR A 192 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 50 " --> pdb=" O THR A 192 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 231 removed outlier: 6.261A pdb=" N PHE A 226 " --> pdb=" O CYS A 359 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU A 361 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP A 228 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N TYR A 363 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLN A 230 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARG A 329 " --> pdb=" O TRP A 358 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ARG A 360 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL A 331 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N TYR A 362 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N HIS A 333 " --> pdb=" O TYR A 362 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS A 261 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE A 330 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY A 262 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA A 315 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL A 264 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS A 287 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR A 316 " --> pdb=" O LYS A 287 " (cutoff:3.500A) 210 hydrogen bonds defined for protein. 603 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: 2.97 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 4080 1.03 - 1.22: 12 1.22 - 1.42: 1795 1.42 - 1.62: 2464 1.62 - 1.81: 35 Bond restraints: 8386 Sorted by residual: bond pdb=" N GLN K 1 " pdb=" CA GLN K 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N GLN K 1 " pdb=" H GLN K 1 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" NH1 ARG A 17 " pdb="HH12 ARG A 17 " ideal model delta sigma weight residual 0.860 0.831 0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C LYS A 120 " pdb=" O LYS A 120 " ideal model delta sigma weight residual 1.234 1.229 0.005 5.00e-03 4.00e+04 1.05e+00 bond pdb=" C ARG A 17 " pdb=" O ARG A 17 " ideal model delta sigma weight residual 1.236 1.246 -0.010 1.15e-02 7.56e+03 7.18e-01 ... (remaining 8381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 14354 1.11 - 2.22: 705 2.22 - 3.33: 34 3.33 - 4.44: 12 4.44 - 5.56: 8 Bond angle restraints: 15113 Sorted by residual: angle pdb=" N SER A 102 " pdb=" CA SER A 102 " pdb=" C SER A 102 " ideal model delta sigma weight residual 113.31 107.75 5.56 2.04e+00 2.40e-01 7.42e+00 angle pdb=" N ASP A 304 " pdb=" CA ASP A 304 " pdb=" C ASP A 304 " ideal model delta sigma weight residual 112.38 110.07 2.31 1.22e+00 6.72e-01 3.60e+00 angle pdb="HH11 ARG A 17 " pdb=" NH1 ARG A 17 " pdb="HH12 ARG A 17 " ideal model delta sigma weight residual 120.00 114.56 5.44 3.00e+00 1.11e-01 3.29e+00 angle pdb=" CA TYR K 111 " pdb=" CB TYR K 111 " pdb=" CG TYR K 111 " ideal model delta sigma weight residual 113.90 117.14 -3.24 1.80e+00 3.09e-01 3.24e+00 angle pdb=" C LYS A 120 " pdb=" N PRO A 121 " pdb=" CA PRO A 121 " ideal model delta sigma weight residual 119.76 117.93 1.83 1.03e+00 9.43e-01 3.16e+00 ... (remaining 15108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 3637 17.71 - 35.42: 254 35.42 - 53.14: 57 53.14 - 70.85: 28 70.85 - 88.56: 5 Dihedral angle restraints: 3981 sinusoidal: 2103 harmonic: 1878 Sorted by residual: dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 95 " pdb=" CB CYS K 95 " ideal model delta sinusoidal sigma weight residual 93.00 145.40 -52.40 1 1.00e+01 1.00e-02 3.74e+01 dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 272 " pdb=" CB CYS A 272 " ideal model delta sinusoidal sigma weight residual 93.00 132.27 -39.27 1 1.00e+01 1.00e-02 2.17e+01 dihedral pdb=" CA GLU A 407 " pdb=" C GLU A 407 " pdb=" N GLU A 408 " pdb=" CA GLU A 408 " ideal model delta harmonic sigma weight residual -180.00 -163.56 -16.44 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 3978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 457 0.030 - 0.060: 125 0.060 - 0.090: 38 0.090 - 0.120: 37 0.120 - 0.150: 3 Chirality restraints: 660 Sorted by residual: chirality pdb=" CA ILE K 31 " pdb=" N ILE K 31 " pdb=" C ILE K 31 " pdb=" CB ILE K 31 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA VAL A 314 " pdb=" N VAL A 314 " pdb=" C VAL A 314 " pdb=" CB VAL A 314 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE K 51 " pdb=" N ILE K 51 " pdb=" C ILE K 51 " pdb=" CB ILE K 51 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 657 not shown) Planarity restraints: 1287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 17 " -0.226 9.50e-02 1.11e+02 9.51e-02 8.15e+01 pdb=" NE ARG A 17 " -0.054 2.00e-02 2.50e+03 pdb=" CZ ARG A 17 " 0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG A 17 " 0.113 2.00e-02 2.50e+03 pdb=" NH2 ARG A 17 " 0.014 2.00e-02 2.50e+03 pdb="HH11 ARG A 17 " 0.007 2.00e-02 2.50e+03 pdb="HH12 ARG A 17 " -0.108 2.00e-02 2.50e+03 pdb="HH21 ARG A 17 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 17 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 101 " 0.034 2.00e-02 2.50e+03 3.93e-02 2.31e+01 pdb=" CG ASN A 101 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 101 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 101 " -0.059 2.00e-02 2.50e+03 pdb="HD21 ASN A 101 " -0.000 2.00e-02 2.50e+03 pdb="HD22 ASN A 101 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 302 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C GLN A 302 " -0.028 2.00e-02 2.50e+03 pdb=" O GLN A 302 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN A 303 " 0.009 2.00e-02 2.50e+03 ... (remaining 1284 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 408 2.18 - 2.78: 16718 2.78 - 3.39: 23243 3.39 - 3.99: 29168 3.99 - 4.60: 45625 Nonbonded interactions: 115162 Sorted by model distance: nonbonded pdb=" HH TYR K 111 " pdb=" OE1 GLU A 201 " model vdw 1.574 2.450 nonbonded pdb="HH12 ARG A 222 " pdb=" O GLY A 348 " model vdw 1.584 2.450 nonbonded pdb="HH22 ARG A 329 " pdb=" OD2 ASP A 353 " model vdw 1.629 2.450 nonbonded pdb=" H CYS A 220 " pdb=" OD2 ASP A 422 " model vdw 1.684 2.450 nonbonded pdb="HE22 GLN A 198 " pdb=" OD2 ASP A 202 " model vdw 1.722 2.450 ... (remaining 115157 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: 0.000 Normalize map: mean=0, sd=1: 3.470 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: 0.160 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.690 Find NCS groups from input model: 0.050 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 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 : 0.002 0.032 4295 Z= 0.162 Angle : 0.512 5.556 5824 Z= 0.277 Chirality : 0.039 0.150 660 Planarity : 0.005 0.074 750 Dihedral : 13.053 88.560 1532 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.37), residues: 554 helix: 1.93 (0.36), residues: 223 sheet: -0.95 (0.48), residues: 116 loop : -0.70 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 305 HIS 0.002 0.000 HIS A 413 PHE 0.012 0.001 PHE A 204 TYR 0.010 0.001 TYR A 419 ARG 0.020 0.001 ARG A 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 51 ILE cc_start: 0.8869 (tp) cc_final: 0.8635 (tp) REVERT: K 106 THR cc_start: 0.8507 (p) cc_final: 0.8031 (p) REVERT: A 111 GLU cc_start: 0.7588 (tp30) cc_final: 0.7118 (tp30) REVERT: A 124 LYS cc_start: 0.6758 (ttpp) cc_final: 0.6311 (ttpp) REVERT: A 198 GLN cc_start: 0.7054 (tm-30) cc_final: 0.6687 (tm-30) REVERT: A 202 ASP cc_start: 0.7569 (m-30) cc_final: 0.6957 (m-30) REVERT: A 302 GLN cc_start: 0.7394 (tm-30) cc_final: 0.7188 (tm-30) REVERT: A 363 TYR cc_start: 0.6083 (t80) cc_final: 0.5739 (t80) REVERT: A 407 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7461 (mm-30) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.4374 time to fit residues: 64.0401 Evaluate side-chains 110 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.154824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.140019 restraints weight = 21109.091| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.80 r_work: 0.3891 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4295 Z= 0.291 Angle : 0.551 5.533 5824 Z= 0.292 Chirality : 0.040 0.154 660 Planarity : 0.004 0.032 750 Dihedral : 4.136 16.850 607 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.86 % Allowed : 8.86 % Favored : 89.28 % 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: 0.68 (0.37), residues: 554 helix: 1.93 (0.35), residues: 227 sheet: -0.93 (0.45), residues: 127 loop : -0.19 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 358 HIS 0.005 0.001 HIS A 290 PHE 0.009 0.002 PHE A 245 TYR 0.008 0.001 TYR A 419 ARG 0.009 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 106 THR cc_start: 0.8514 (p) cc_final: 0.8039 (p) REVERT: A 111 GLU cc_start: 0.7666 (tp30) cc_final: 0.7151 (tp30) REVERT: A 124 LYS cc_start: 0.6932 (ttpp) cc_final: 0.6283 (mtpp) REVERT: A 198 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6847 (tm-30) REVERT: A 202 ASP cc_start: 0.7679 (m-30) cc_final: 0.6981 (m-30) REVERT: A 363 TYR cc_start: 0.6287 (t80) cc_final: 0.5993 (t80) REVERT: A 407 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7325 (mm-30) outliers start: 8 outliers final: 7 residues processed: 121 average time/residue: 0.4290 time to fit residues: 62.1004 Evaluate side-chains 119 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 267 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 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 101 ASN A 160 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.152353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.137050 restraints weight = 21263.120| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.82 r_work: 0.3851 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 4295 Z= 0.375 Angle : 0.591 5.959 5824 Z= 0.315 Chirality : 0.042 0.146 660 Planarity : 0.005 0.046 750 Dihedral : 4.251 15.715 607 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.33 % Allowed : 11.42 % Favored : 86.25 % 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: 0.47 (0.36), residues: 554 helix: 1.76 (0.35), residues: 227 sheet: -0.86 (0.46), residues: 128 loop : -0.46 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 358 HIS 0.005 0.001 HIS A 333 PHE 0.030 0.002 PHE A 204 TYR 0.010 0.002 TYR A 419 ARG 0.008 0.001 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 33 ARG cc_start: 0.8436 (ptt90) cc_final: 0.8186 (ptt90) REVERT: K 106 THR cc_start: 0.8541 (p) cc_final: 0.7966 (p) REVERT: K 108 GLU cc_start: 0.7487 (mp0) cc_final: 0.7124 (mp0) REVERT: A 111 GLU cc_start: 0.7694 (tp30) cc_final: 0.7253 (tp30) REVERT: A 124 LYS cc_start: 0.7191 (ttpp) cc_final: 0.6339 (mtpp) REVERT: A 202 ASP cc_start: 0.7670 (m-30) cc_final: 0.6963 (m-30) REVERT: A 363 TYR cc_start: 0.6429 (t80) cc_final: 0.6093 (t80) REVERT: A 408 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7119 (tm-30) outliers start: 10 outliers final: 10 residues processed: 121 average time/residue: 0.4182 time to fit residues: 61.3439 Evaluate side-chains 122 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 32 ASN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 281 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 30 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 54 optimal weight: 0.0770 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 overall best weight: 0.6136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.152211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.137563 restraints weight = 21118.265| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.84 r_work: 0.3846 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4295 Z= 0.284 Angle : 0.536 5.498 5824 Z= 0.283 Chirality : 0.040 0.146 660 Planarity : 0.004 0.037 750 Dihedral : 4.193 15.627 607 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.10 % Allowed : 13.29 % Favored : 84.62 % 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: 0.60 (0.37), residues: 554 helix: 2.01 (0.35), residues: 228 sheet: -0.96 (0.44), residues: 130 loop : -0.46 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 165 HIS 0.004 0.001 HIS A 333 PHE 0.021 0.002 PHE A 204 TYR 0.011 0.002 TYR K 111 ARG 0.003 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 33 ARG cc_start: 0.8411 (ptt90) cc_final: 0.8172 (ptt90) REVERT: K 106 THR cc_start: 0.8546 (p) cc_final: 0.7789 (p) REVERT: K 108 GLU cc_start: 0.7625 (mp0) cc_final: 0.7116 (mp0) REVERT: A 111 GLU cc_start: 0.7663 (tp30) cc_final: 0.7206 (tp30) REVERT: A 124 LYS cc_start: 0.7160 (ttpp) cc_final: 0.6903 (mtpp) REVERT: A 165 TRP cc_start: 0.8033 (m100) cc_final: 0.7591 (m100) REVERT: A 202 ASP cc_start: 0.7236 (m-30) cc_final: 0.6809 (m-30) REVERT: A 363 TYR cc_start: 0.6526 (t80) cc_final: 0.6178 (t80) REVERT: A 408 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7104 (tm-30) outliers start: 9 outliers final: 8 residues processed: 120 average time/residue: 0.4624 time to fit residues: 65.7957 Evaluate side-chains 121 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 32 ASN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 45 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 14 optimal weight: 0.0270 chunk 12 optimal weight: 0.0980 chunk 13 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 43 optimal weight: 0.4980 overall best weight: 0.2638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.153632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.138996 restraints weight = 21060.814| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.86 r_work: 0.3866 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4295 Z= 0.173 Angle : 0.488 5.051 5824 Z= 0.253 Chirality : 0.039 0.145 660 Planarity : 0.004 0.033 750 Dihedral : 3.979 15.116 607 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.80 % Allowed : 13.75 % Favored : 83.45 % 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: 0.92 (0.37), residues: 554 helix: 2.29 (0.36), residues: 229 sheet: -0.86 (0.45), residues: 130 loop : -0.29 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 305 HIS 0.002 0.001 HIS A 413 PHE 0.020 0.001 PHE A 204 TYR 0.010 0.001 TYR A 419 ARG 0.005 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 106 THR cc_start: 0.8529 (p) cc_final: 0.7662 (p) REVERT: K 108 GLU cc_start: 0.7592 (mp0) cc_final: 0.7013 (mp0) REVERT: A 111 GLU cc_start: 0.7680 (tp30) cc_final: 0.7208 (tp30) REVERT: A 124 LYS cc_start: 0.6999 (ttpp) cc_final: 0.6713 (mtpp) REVERT: A 165 TRP cc_start: 0.8058 (m100) cc_final: 0.7608 (m100) REVERT: A 202 ASP cc_start: 0.7270 (m-30) cc_final: 0.6801 (m-30) REVERT: A 363 TYR cc_start: 0.6502 (t80) cc_final: 0.5947 (t80) REVERT: A 407 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7247 (mm-30) REVERT: A 408 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7084 (tm-30) outliers start: 12 outliers final: 9 residues processed: 118 average time/residue: 0.4919 time to fit residues: 69.1764 Evaluate side-chains 120 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 32 ASN Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 312 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 44 optimal weight: 0.0070 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.150337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.135462 restraints weight = 21319.051| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.88 r_work: 0.3820 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4295 Z= 0.302 Angle : 0.538 5.462 5824 Z= 0.283 Chirality : 0.040 0.142 660 Planarity : 0.004 0.033 750 Dihedral : 4.144 15.161 607 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.56 % Allowed : 14.45 % Favored : 82.98 % 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: 0.76 (0.37), residues: 554 helix: 2.14 (0.35), residues: 230 sheet: -1.01 (0.44), residues: 135 loop : -0.26 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 358 HIS 0.005 0.001 HIS A 333 PHE 0.013 0.002 PHE A 204 TYR 0.013 0.002 TYR A 419 ARG 0.004 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 82 MET cc_start: 0.7146 (mtt) cc_final: 0.6775 (mtt) REVERT: K 106 THR cc_start: 0.8584 (p) cc_final: 0.7649 (p) REVERT: K 108 GLU cc_start: 0.7642 (mp0) cc_final: 0.7051 (mp0) REVERT: A 111 GLU cc_start: 0.7672 (tp30) cc_final: 0.7219 (tp30) REVERT: A 165 TRP cc_start: 0.8046 (m100) cc_final: 0.7666 (m100) REVERT: A 202 ASP cc_start: 0.7278 (m-30) cc_final: 0.6800 (m-30) REVERT: A 363 TYR cc_start: 0.6733 (t80) cc_final: 0.6072 (t80) REVERT: A 407 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7183 (mm-30) REVERT: A 408 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7094 (tm-30) outliers start: 11 outliers final: 9 residues processed: 120 average time/residue: 0.5469 time to fit residues: 78.3431 Evaluate side-chains 118 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 32 ASN Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 9 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.149845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.134878 restraints weight = 21420.498| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.90 r_work: 0.3814 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4295 Z= 0.324 Angle : 0.550 5.490 5824 Z= 0.291 Chirality : 0.041 0.159 660 Planarity : 0.004 0.032 750 Dihedral : 4.183 15.237 607 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.80 % Allowed : 14.45 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.37), residues: 554 helix: 2.04 (0.36), residues: 230 sheet: -1.01 (0.43), residues: 135 loop : -0.32 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 358 HIS 0.005 0.001 HIS A 333 PHE 0.013 0.002 PHE A 204 TYR 0.013 0.002 TYR A 419 ARG 0.004 0.001 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 82 MET cc_start: 0.7178 (mtt) cc_final: 0.6841 (mtt) REVERT: K 106 THR cc_start: 0.8594 (p) cc_final: 0.7601 (p) REVERT: K 108 GLU cc_start: 0.7651 (mp0) cc_final: 0.7080 (mp0) REVERT: A 111 GLU cc_start: 0.7676 (tp30) cc_final: 0.7226 (tp30) REVERT: A 165 TRP cc_start: 0.8060 (m100) cc_final: 0.7687 (m100) REVERT: A 202 ASP cc_start: 0.7286 (m-30) cc_final: 0.6795 (m-30) REVERT: A 363 TYR cc_start: 0.6783 (t80) cc_final: 0.6078 (t80) REVERT: A 407 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7148 (mm-30) REVERT: A 408 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7090 (tm-30) outliers start: 12 outliers final: 10 residues processed: 117 average time/residue: 0.4752 time to fit residues: 66.1458 Evaluate side-chains 121 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 32 ASN Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 312 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 chunk 35 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 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 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.150310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.135493 restraints weight = 21618.746| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.85 r_work: 0.3820 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4295 Z= 0.261 Angle : 0.519 5.284 5824 Z= 0.272 Chirality : 0.039 0.148 660 Planarity : 0.004 0.034 750 Dihedral : 4.118 14.971 607 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.03 % Allowed : 14.45 % Favored : 82.52 % 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: 0.73 (0.37), residues: 554 helix: 2.17 (0.36), residues: 230 sheet: -0.85 (0.45), residues: 125 loop : -0.55 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 358 HIS 0.003 0.001 HIS A 333 PHE 0.014 0.002 PHE A 204 TYR 0.012 0.001 TYR A 419 ARG 0.004 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 82 MET cc_start: 0.7143 (mtt) cc_final: 0.6810 (mtt) REVERT: K 106 THR cc_start: 0.8604 (p) cc_final: 0.7554 (p) REVERT: K 108 GLU cc_start: 0.7584 (mp0) cc_final: 0.6981 (mp0) REVERT: A 73 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8157 (m) REVERT: A 111 GLU cc_start: 0.7632 (tp30) cc_final: 0.7181 (tp30) REVERT: A 165 TRP cc_start: 0.8048 (m100) cc_final: 0.7722 (m100) REVERT: A 202 ASP cc_start: 0.7291 (m-30) cc_final: 0.6798 (m-30) REVERT: A 363 TYR cc_start: 0.6776 (t80) cc_final: 0.6064 (t80) REVERT: A 407 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7128 (mm-30) REVERT: A 408 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7056 (tm-30) outliers start: 13 outliers final: 10 residues processed: 118 average time/residue: 0.4614 time to fit residues: 64.9614 Evaluate side-chains 120 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 32 ASN Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 312 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 25 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 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 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.150287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.135419 restraints weight = 21641.911| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.87 r_work: 0.3817 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4295 Z= 0.268 Angle : 0.528 5.465 5824 Z= 0.278 Chirality : 0.040 0.143 660 Planarity : 0.004 0.031 750 Dihedral : 4.126 14.987 607 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.10 % Allowed : 15.38 % Favored : 82.52 % 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: 0.73 (0.37), residues: 554 helix: 2.17 (0.36), residues: 230 sheet: -0.83 (0.45), residues: 125 loop : -0.56 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 358 HIS 0.004 0.001 HIS A 333 PHE 0.012 0.002 PHE A 204 TYR 0.012 0.001 TYR K 111 ARG 0.004 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 82 MET cc_start: 0.7138 (mtt) cc_final: 0.6813 (mtt) REVERT: K 106 THR cc_start: 0.8616 (p) cc_final: 0.7587 (p) REVERT: K 108 GLU cc_start: 0.7585 (mp0) cc_final: 0.6991 (mp0) REVERT: A 73 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.8152 (m) REVERT: A 111 GLU cc_start: 0.7658 (tp30) cc_final: 0.7197 (tp30) REVERT: A 165 TRP cc_start: 0.8060 (m100) cc_final: 0.7738 (m100) REVERT: A 175 ARG cc_start: 0.8276 (mtp85) cc_final: 0.7976 (mtt-85) REVERT: A 202 ASP cc_start: 0.7299 (m-30) cc_final: 0.6760 (m-30) REVERT: A 363 TYR cc_start: 0.6823 (t80) cc_final: 0.6070 (t80) REVERT: A 407 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7093 (mm-30) REVERT: A 408 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7033 (tm-30) outliers start: 9 outliers final: 7 residues processed: 114 average time/residue: 0.4444 time to fit residues: 61.0681 Evaluate side-chains 118 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 32 ASN Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 10 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 chunk 22 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.151228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.136406 restraints weight = 21363.308| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.90 r_work: 0.3827 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4295 Z= 0.196 Angle : 0.501 5.029 5824 Z= 0.259 Chirality : 0.039 0.142 660 Planarity : 0.004 0.031 750 Dihedral : 4.003 14.504 607 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.17 % Allowed : 16.08 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.37), residues: 554 helix: 2.36 (0.36), residues: 230 sheet: -0.71 (0.47), residues: 120 loop : -0.60 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 358 HIS 0.002 0.001 HIS A 413 PHE 0.013 0.001 PHE A 204 TYR 0.012 0.001 TYR K 111 ARG 0.005 0.000 ARG A 182 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1108 Ramachandran restraints generated. 554 Oldfield, 0 Emsley, 554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 338 is missing expected H atoms. Skipping. Residue ILE 375 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue VAL 379 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LEU 382 is missing expected H atoms. Skipping. Residue LYS 385 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue THR 438 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 82 MET cc_start: 0.6998 (mtt) cc_final: 0.6688 (mtt) REVERT: K 106 THR cc_start: 0.8589 (p) cc_final: 0.7611 (p) REVERT: K 108 GLU cc_start: 0.7603 (mp0) cc_final: 0.7014 (mp0) REVERT: A 111 GLU cc_start: 0.7697 (tp30) cc_final: 0.7229 (tp30) REVERT: A 165 TRP cc_start: 0.8054 (m100) cc_final: 0.7729 (m100) REVERT: A 175 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7966 (mtt-85) REVERT: A 202 ASP cc_start: 0.7160 (m-30) cc_final: 0.6638 (m-30) REVERT: A 363 TYR cc_start: 0.6799 (t80) cc_final: 0.6033 (t80) REVERT: A 407 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7048 (mm-30) REVERT: A 408 GLU cc_start: 0.7463 (tm-30) cc_final: 0.6954 (tm-30) outliers start: 5 outliers final: 5 residues processed: 112 average time/residue: 0.4524 time to fit residues: 60.5490 Evaluate side-chains 114 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 32 ASN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain A residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 7 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 35 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 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 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.149024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.134275 restraints weight = 21419.277| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.83 r_work: 0.3804 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4295 Z= 0.325 Angle : 0.542 5.389 5824 Z= 0.287 Chirality : 0.041 0.145 660 Planarity : 0.004 0.032 750 Dihedral : 4.172 15.129 607 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.86 % Allowed : 15.85 % Favored : 82.28 % 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: 0.68 (0.37), residues: 554 helix: 2.19 (0.35), residues: 230 sheet: -1.00 (0.44), residues: 125 loop : -0.56 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 358 HIS 0.005 0.001 HIS A 333 PHE 0.011 0.002 PHE K 67 TYR 0.012 0.002 TYR A 419 ARG 0.004 0.001 ARG A 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5850.96 seconds wall clock time: 103 minutes 45.22 seconds (6225.22 seconds total)