Starting phenix.real_space_refine on Wed Feb 12 20:42:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rla_19336/02_2025/8rla_19336.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rla_19336/02_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_19336/02_2025/8rla_19336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rla_19336/02_2025/8rla_19336.map" model { file = "/net/cci-nas-00/data/ceres_data/8rla_19336/02_2025/8rla_19336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rla_19336/02_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-5592/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: 4.41, per 1000 atoms: 0.53 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: 2.02 Conformation dependent library (CDL) restraints added in 668.9 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: 0.63 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: 2.68 Time building geometry restraints manager: 2.42 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: 2.130 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: 0.140 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.240 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.640 ------------------------------------------------------------------------------- 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 : 0.731 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: 0.4390 time to fit residues: 64.4971 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 : 0.683 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.140020 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 : 0.636 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: 0.8038 (p) REVERT: A 111 GLU cc_start: 0.7665 (tp30) cc_final: 0.7151 (tp30) REVERT: A 124 LYS cc_start: 0.6933 (ttpp) cc_final: 0.6283 (mtpp) REVERT: A 198 GLN cc_start: 0.7274 (tm-30) cc_final: 0.6846 (tm-30) REVERT: A 202 ASP cc_start: 0.7681 (m-30) cc_final: 0.6983 (m-30) REVERT: A 363 TYR cc_start: 0.6289 (t80) cc_final: 0.5994 (t80) REVERT: A 407 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7323 (mm-30) outliers start: 8 outliers final: 7 residues processed: 121 average time/residue: 0.4489 time to fit residues: 64.8542 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 : 0.673 ------------------------------------------------------------------------------- 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: 0.9980 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4142 r_free = 0.4142 target = 0.152204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.136893 restraints weight = 21301.004| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.82 r_work: 0.3850 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 4295 Z= 0.381 Angle : 0.591 5.734 5824 Z= 0.318 Chirality : 0.042 0.151 660 Planarity : 0.005 0.035 750 Dihedral : 4.267 15.802 607 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.33 % Allowed : 11.66 % Favored : 86.01 % 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: 0.48 (0.36), residues: 554 helix: 1.76 (0.35), residues: 227 sheet: -0.86 (0.46), residues: 128 loop : -0.45 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 358 HIS 0.005 0.001 HIS A 333 PHE 0.027 0.002 PHE A 204 TYR 0.010 0.002 TYR A 419 ARG 0.007 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 129 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.668 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: K 33 ARG cc_start: 0.8423 (ptt90) cc_final: 0.8150 (ptt90) REVERT: K 106 THR cc_start: 0.8495 (p) cc_final: 0.7943 (p) REVERT: K 108 GLU cc_start: 0.7468 (mp0) cc_final: 0.7108 (mp0) REVERT: A 111 GLU cc_start: 0.7702 (tp30) cc_final: 0.7255 (tp30) REVERT: A 124 LYS cc_start: 0.7205 (ttpp) cc_final: 0.6352 (mtpp) REVERT: A 198 GLN cc_start: 0.7219 (tm-30) cc_final: 0.6605 (tm-30) REVERT: A 202 ASP cc_start: 0.7662 (m-30) cc_final: 0.6762 (m-30) REVERT: A 363 TYR cc_start: 0.6452 (t80) cc_final: 0.6111 (t80) REVERT: A 408 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7104 (tm-30) outliers start: 10 outliers final: 10 residues processed: 122 average time/residue: 0.4355 time to fit residues: 63.6495 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 : 0.603 ------------------------------------------------------------------------------- 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: 0.4980 chunk 54 optimal weight: 0.0170 chunk 29 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.3616 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.153815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.139275 restraints weight = 21164.292| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.83 r_work: 0.3874 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4295 Z= 0.204 Angle : 0.509 5.302 5824 Z= 0.265 Chirality : 0.039 0.148 660 Planarity : 0.004 0.046 750 Dihedral : 4.082 16.069 607 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.40 % Allowed : 13.05 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.37), residues: 554 helix: 2.23 (0.36), residues: 228 sheet: -0.91 (0.45), residues: 130 loop : -0.28 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 358 HIS 0.003 0.001 HIS A 167 PHE 0.023 0.001 PHE A 204 TYR 0.011 0.001 TYR K 111 ARG 0.008 0.000 ARG A 182 *********************** 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 115 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.607 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 82 MET cc_start: 0.6818 (mtt) cc_final: 0.6575 (mtt) REVERT: K 106 THR cc_start: 0.8561 (p) cc_final: 0.7820 (p) REVERT: K 108 GLU cc_start: 0.7588 (mp0) cc_final: 0.7099 (mp0) REVERT: A 111 GLU cc_start: 0.7698 (tp30) cc_final: 0.7236 (tp30) REVERT: A 124 LYS cc_start: 0.7017 (ttpp) cc_final: 0.6227 (mtpp) REVERT: A 198 GLN cc_start: 0.7104 (tm-30) cc_final: 0.6508 (tm-30) REVERT: A 202 ASP cc_start: 0.7509 (m-30) cc_final: 0.6642 (m-30) REVERT: A 302 GLN cc_start: 0.7017 (tm-30) cc_final: 0.6107 (tm-30) REVERT: A 306 MET cc_start: 0.8548 (mmm) cc_final: 0.8213 (mmm) REVERT: A 363 TYR cc_start: 0.6383 (t80) cc_final: 0.6045 (t80) REVERT: A 408 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7069 (tm-30) outliers start: 6 outliers final: 6 residues processed: 110 average time/residue: 0.4166 time to fit residues: 55.5440 Evaluate side-chains 113 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 45 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.0980 chunk 13 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 0.0980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.153141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.138531 restraints weight = 21034.558| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.84 r_work: 0.3858 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4295 Z= 0.216 Angle : 0.497 5.230 5824 Z= 0.259 Chirality : 0.039 0.144 660 Planarity : 0.004 0.038 750 Dihedral : 4.022 15.083 607 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.86 % Allowed : 14.69 % 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: 0.96 (0.37), residues: 554 helix: 2.35 (0.36), residues: 228 sheet: -0.93 (0.45), residues: 130 loop : -0.21 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 165 HIS 0.003 0.001 HIS A 333 PHE 0.017 0.001 PHE A 204 TYR 0.011 0.001 TYR A 419 ARG 0.007 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 118 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.606 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: 0.8550 (p) cc_final: 0.7703 (p) REVERT: K 108 GLU cc_start: 0.7614 (mp0) cc_final: 0.6980 (mp0) REVERT: A 111 GLU cc_start: 0.7638 (tp30) cc_final: 0.7190 (tp30) REVERT: A 124 LYS cc_start: 0.7066 (ttpp) cc_final: 0.6375 (mtpp) REVERT: A 198 GLN cc_start: 0.7041 (tm-30) cc_final: 0.6388 (tm-30) REVERT: A 202 ASP cc_start: 0.7416 (m-30) cc_final: 0.6487 (m-30) REVERT: A 363 TYR cc_start: 0.6384 (t80) cc_final: 0.5920 (t80) REVERT: A 407 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7188 (mm-30) REVERT: A 408 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7127 (tm-30) outliers start: 8 outliers final: 7 residues processed: 112 average time/residue: 0.4261 time to fit residues: 58.3886 Evaluate side-chains 122 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 A residue 27 ASP Chi-restraints excluded: chain A residue 77 SER 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: 0.5980 chunk 24 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 9 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 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.151436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.136697 restraints weight = 21337.416| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.85 r_work: 0.3838 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.3009 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= 0.260 Angle : 0.515 5.338 5824 Z= 0.271 Chirality : 0.040 0.146 660 Planarity : 0.004 0.037 750 Dihedral : 4.098 15.090 607 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: 0.87 (0.37), residues: 554 helix: 2.26 (0.36), residues: 230 sheet: -0.93 (0.45), residues: 130 loop : -0.28 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 165 HIS 0.004 0.001 HIS A 333 PHE 0.016 0.002 PHE A 204 TYR 0.012 0.001 TYR A 419 ARG 0.008 0.001 ARG A 182 *********************** 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 131 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.607 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: K 106 THR cc_start: 0.8589 (p) cc_final: 0.7661 (p) REVERT: K 108 GLU cc_start: 0.7630 (mp0) cc_final: 0.7057 (mp0) REVERT: A 111 GLU cc_start: 0.7660 (tp30) cc_final: 0.7201 (tp30) REVERT: A 202 ASP cc_start: 0.7378 (m-30) cc_final: 0.6696 (m-30) REVERT: A 363 TYR cc_start: 0.6516 (t80) cc_final: 0.6043 (t80) REVERT: A 407 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7166 (mm-30) REVERT: A 408 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7094 (tm-30) outliers start: 11 outliers final: 8 residues processed: 124 average time/residue: 0.4792 time to fit residues: 70.4093 Evaluate side-chains 117 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 281 CYS 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: 0.6980 chunk 52 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.0370 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 10 optimal weight: 0.1980 chunk 49 optimal weight: 10.0000 overall best weight: 0.4058 ------------------------------------------------------------------------------- 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 = 0.4134 r_free = 0.4134 target = 0.151798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.137134 restraints weight = 21452.750| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.86 r_work: 0.3842 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4295 Z= 0.219 Angle : 0.498 5.101 5824 Z= 0.259 Chirality : 0.039 0.146 660 Planarity : 0.004 0.031 750 Dihedral : 4.001 14.845 607 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.63 % Allowed : 15.15 % Favored : 83.22 % 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: 0.96 (0.37), residues: 554 helix: 2.32 (0.35), residues: 230 sheet: -0.85 (0.45), residues: 130 loop : -0.24 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.002 0.001 HIS A 333 PHE 0.013 0.001 PHE A 204 TYR 0.011 0.001 TYR A 419 ARG 0.003 0.000 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 116 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.631 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: 0.7030 (mtt) cc_final: 0.6640 (mtt) REVERT: K 106 THR cc_start: 0.8596 (p) cc_final: 0.7611 (p) REVERT: K 108 GLU cc_start: 0.7624 (mp0) cc_final: 0.7040 (mp0) REVERT: A 111 GLU cc_start: 0.7605 (tp30) cc_final: 0.7153 (tp30) REVERT: A 175 ARG cc_start: 0.8245 (mtp85) cc_final: 0.7937 (mtt-85) REVERT: A 202 ASP cc_start: 0.7265 (m-30) cc_final: 0.6828 (m-30) REVERT: A 363 TYR cc_start: 0.6623 (t80) cc_final: 0.5952 (t80) REVERT: A 407 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7171 (mm-30) REVERT: A 408 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7063 (tm-30) outliers start: 7 outliers final: 7 residues processed: 112 average time/residue: 0.4259 time to fit residues: 57.4783 Evaluate side-chains 114 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 27 ASP Chi-restraints excluded: chain A residue 34 GLN 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: 2.9990 chunk 23 optimal weight: 0.3980 chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.150589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.135576 restraints weight = 21678.618| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.94 r_work: 0.3820 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3369 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= 0.281 Angle : 0.519 5.246 5824 Z= 0.274 Chirality : 0.040 0.166 660 Planarity : 0.004 0.031 750 Dihedral : 4.064 14.845 607 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.33 % Allowed : 14.92 % 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: 0.85 (0.37), residues: 554 helix: 2.24 (0.36), residues: 230 sheet: -0.91 (0.45), residues: 130 loop : -0.32 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 358 HIS 0.004 0.001 HIS A 333 PHE 0.011 0.002 PHE A 204 TYR 0.012 0.001 TYR A 419 ARG 0.005 0.001 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 120 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.677 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: K 82 MET cc_start: 0.7071 (mtt) cc_final: 0.6696 (mtt) REVERT: K 106 THR cc_start: 0.8604 (p) cc_final: 0.7606 (p) REVERT: K 108 GLU cc_start: 0.7674 (mp0) cc_final: 0.7084 (mp0) REVERT: A 111 GLU cc_start: 0.7659 (tp30) cc_final: 0.7198 (tp30) REVERT: A 175 ARG cc_start: 0.8255 (mtp85) cc_final: 0.7952 (mtt-85) REVERT: A 202 ASP cc_start: 0.7276 (m-30) cc_final: 0.6836 (m-30) REVERT: A 363 TYR cc_start: 0.6728 (t80) cc_final: 0.6027 (t80) REVERT: A 407 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7154 (mm-30) REVERT: A 408 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7055 (tm-30) outliers start: 10 outliers final: 8 residues processed: 113 average time/residue: 0.4756 time to fit residues: 63.9295 Evaluate side-chains 115 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 281 CYS 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: 0.2980 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 335 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.150593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.135784 restraints weight = 21775.940| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.89 r_work: 0.3825 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4295 Z= 0.262 Angle : 0.511 5.195 5824 Z= 0.268 Chirality : 0.039 0.147 660 Planarity : 0.004 0.028 750 Dihedral : 4.058 14.988 607 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.56 % Allowed : 14.92 % 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: 0.85 (0.37), residues: 554 helix: 2.29 (0.36), residues: 230 sheet: -0.73 (0.46), residues: 120 loop : -0.58 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 358 HIS 0.003 0.001 HIS A 333 PHE 0.012 0.002 PHE A 204 TYR 0.012 0.001 TYR A 419 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 121 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.614 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: 0.7106 (mtt) cc_final: 0.6748 (mtt) REVERT: A 111 GLU cc_start: 0.7644 (tp30) cc_final: 0.7188 (tp30) REVERT: A 175 ARG cc_start: 0.8257 (mtp85) cc_final: 0.7960 (mtt-85) REVERT: A 363 TYR cc_start: 0.6748 (t80) cc_final: 0.6011 (t80) REVERT: A 407 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7114 (mm-30) REVERT: A 408 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7031 (tm-30) outliers start: 11 outliers final: 10 residues processed: 114 average time/residue: 0.4619 time to fit residues: 62.6666 Evaluate side-chains 117 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 77 SER Chi-restraints excluded: chain A residue 281 CYS 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: 0.9990 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.150291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.135918 restraints weight = 21460.386| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.83 r_work: 0.3825 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 4295 Z= 0.289 Angle : 1.095 59.200 5824 Z= 0.655 Chirality : 0.041 0.299 660 Planarity : 0.004 0.029 750 Dihedral : 4.063 14.937 607 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.63 % Allowed : 16.32 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.37), residues: 554 helix: 2.32 (0.36), residues: 230 sheet: -0.73 (0.46), residues: 120 loop : -0.58 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 165 HIS 0.003 0.001 HIS A 333 PHE 0.011 0.002 PHE A 204 TYR 0.012 0.001 TYR A 419 ARG 0.003 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 114 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.617 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: K 82 MET cc_start: 0.7091 (mtt) cc_final: 0.6742 (mtt) REVERT: A 111 GLU cc_start: 0.7635 (tp30) cc_final: 0.7182 (tp30) REVERT: A 175 ARG cc_start: 0.8255 (mtp85) cc_final: 0.7956 (mtt-85) REVERT: A 363 TYR cc_start: 0.6748 (t80) cc_final: 0.6017 (t80) REVERT: A 407 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7112 (mm-30) REVERT: A 408 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7004 (tm-30) outliers start: 7 outliers final: 7 residues processed: 110 average time/residue: 0.4337 time to fit residues: 57.3800 Evaluate side-chains 113 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 35 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 14 optimal weight: 20.0000 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 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.150283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.135841 restraints weight = 21510.979| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.84 r_work: 0.3825 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 4295 Z= 0.289 Angle : 1.095 59.200 5824 Z= 0.655 Chirality : 0.041 0.299 660 Planarity : 0.004 0.029 750 Dihedral : 4.063 14.937 607 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.63 % Allowed : 16.32 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.37), residues: 554 helix: 2.32 (0.36), residues: 230 sheet: -0.73 (0.46), residues: 120 loop : -0.58 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 165 HIS 0.003 0.001 HIS A 333 PHE 0.011 0.002 PHE A 204 TYR 0.012 0.001 TYR A 419 ARG 0.003 0.000 ARG A 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4967.06 seconds wall clock time: 88 minutes 3.91 seconds (5283.91 seconds total)