Starting phenix.real_space_refine on Wed Sep 17 11:13:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rla_19336/09_2025/8rla_19336.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rla_19336/09_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_19336/09_2025/8rla_19336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rla_19336/09_2025/8rla_19336.map" model { file = "/net/cci-nas-00/data/ceres_data/8rla_19336/09_2025/8rla_19336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rla_19336/09_2025/8rla_19336.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 2, 'ASN:plan1': 1} 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: {'ARG:plan': 7, 'GLU:plan': 6, 'ASP:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1} 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: 1.99, per 1000 atoms: 0.24 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: 0.94 Conformation dependent library (CDL) restraints added in 362.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.25 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: 1.83 Time building geometry restraints manager: 1.27 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: 4.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.610 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.540 ------------------------------------------------------------------------------- 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 4301 Z= 0.108 Angle : 0.536 8.208 5834 Z= 0.279 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 : 10.48 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.020 0.001 ARG A 17 TYR 0.010 0.001 TYR A 419 PHE 0.012 0.001 PHE A 204 TRP 0.006 0.001 TRP A 305 HIS 0.002 0.000 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 4295) covalent geometry : angle 0.51212 ( 5824) SS BOND : bond 0.00363 ( 2) SS BOND : angle 1.16195 ( 4) hydrogen bonds : bond 0.16495 ( 205) hydrogen bonds : angle 6.65871 ( 603) metal coordination : bond 0.00264 ( 4) metal coordination : angle 4.93319 ( 6) *********************** 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 : 0.217 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: 0.2262 time to fit residues: 32.9939 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 : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.1980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.156898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.141862 restraints weight = 21126.012| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.86 r_work: 0.3916 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4301 Z= 0.145 Angle : 0.549 8.516 5834 Z= 0.279 Chirality : 0.039 0.161 660 Planarity : 0.004 0.037 750 Dihedral : 4.009 17.051 607 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.93 % Allowed : 9.32 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.37), residues: 554 helix: 2.08 (0.35), residues: 227 sheet: -0.84 (0.47), residues: 119 loop : -0.39 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 182 TYR 0.007 0.001 TYR A 419 PHE 0.009 0.001 PHE A 204 TRP 0.003 0.001 TRP A 358 HIS 0.004 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4295) covalent geometry : angle 0.52987 ( 5824) SS BOND : bond 0.00220 ( 2) SS BOND : angle 0.71258 ( 4) hydrogen bonds : bond 0.04191 ( 205) hydrogen bonds : angle 4.99140 ( 603) metal coordination : bond 0.00567 ( 4) metal coordination : angle 4.53170 ( 6) *********************** 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 120 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.206 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: 0.8574 (p) cc_final: 0.8104 (p) REVERT: A 111 GLU cc_start: 0.7629 (tp30) cc_final: 0.7070 (tp30) REVERT: A 124 LYS cc_start: 0.6749 (ttpp) cc_final: 0.6103 (mtpp) REVERT: A 198 GLN cc_start: 0.7259 (tm-30) cc_final: 0.6778 (tm-30) REVERT: A 202 ASP cc_start: 0.7701 (m-30) cc_final: 0.6845 (m-30) REVERT: A 363 TYR cc_start: 0.6200 (t80) cc_final: 0.5935 (t80) REVERT: A 407 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7316 (mm-30) outliers start: 4 outliers final: 3 residues processed: 116 average time/residue: 0.2121 time to fit residues: 29.1814 Evaluate side-chains 111 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 77 SER 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 54 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 49 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4135 r_free = 0.4135 target = 0.151878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.136706 restraints weight = 21152.196| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.82 r_work: 0.3847 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 4301 Z= 0.254 Angle : 0.634 11.059 5834 Z= 0.321 Chirality : 0.042 0.142 660 Planarity : 0.005 0.047 750 Dihedral : 4.284 16.035 607 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.56 % Allowed : 10.96 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.36), residues: 554 helix: 1.89 (0.35), residues: 227 sheet: -0.99 (0.45), residues: 135 loop : -0.38 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 182 TYR 0.012 0.002 TYR A 419 PHE 0.014 0.002 PHE A 26 TRP 0.005 0.001 TRP A 358 HIS 0.005 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00574 ( 4295) covalent geometry : angle 0.60116 ( 5824) SS BOND : bond 0.00181 ( 2) SS BOND : angle 0.91628 ( 4) hydrogen bonds : bond 0.04611 ( 205) hydrogen bonds : angle 4.91244 ( 603) metal coordination : bond 0.00981 ( 4) metal coordination : angle 6.32883 ( 6) *********************** 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 136 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.223 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: symmetry clash REVERT: K 33 ARG cc_start: 0.8261 (ptt90) cc_final: 0.8039 (ptt90) REVERT: K 106 THR cc_start: 0.8651 (p) cc_final: 0.7947 (p) REVERT: K 108 GLU cc_start: 0.7650 (mp0) cc_final: 0.7180 (mp0) REVERT: A 111 GLU cc_start: 0.7701 (tp30) cc_final: 0.7260 (tp30) REVERT: A 124 LYS cc_start: 0.7190 (ttpp) cc_final: 0.6668 (mtpp) REVERT: A 198 GLN cc_start: 0.7107 (tm-30) cc_final: 0.6471 (tm-30) REVERT: A 202 ASP cc_start: 0.7617 (m-30) cc_final: 0.6694 (m-30) REVERT: A 363 TYR cc_start: 0.6396 (t80) cc_final: 0.6020 (t80) REVERT: A 407 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7307 (mm-30) outliers start: 11 outliers final: 10 residues processed: 128 average time/residue: 0.2276 time to fit residues: 34.4291 Evaluate side-chains 124 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 312 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.151611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.136836 restraints weight = 21411.680| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.85 r_work: 0.3834 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4301 Z= 0.218 Angle : 0.586 10.429 5834 Z= 0.296 Chirality : 0.041 0.147 660 Planarity : 0.004 0.038 750 Dihedral : 4.278 16.087 607 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.56 % Allowed : 13.05 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.37), residues: 554 helix: 1.95 (0.35), residues: 227 sheet: -0.96 (0.45), residues: 130 loop : -0.51 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 182 TYR 0.010 0.002 TYR A 343 PHE 0.011 0.002 PHE A 26 TRP 0.005 0.001 TRP A 358 HIS 0.004 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 4295) covalent geometry : angle 0.55727 ( 5824) SS BOND : bond 0.00160 ( 2) SS BOND : angle 0.73363 ( 4) hydrogen bonds : bond 0.04095 ( 205) hydrogen bonds : angle 4.72706 ( 603) metal coordination : bond 0.00798 ( 4) metal coordination : angle 5.62104 ( 6) *********************** 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 129 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.149 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 108 GLU cc_start: 0.7713 (mp0) cc_final: 0.7116 (mp0) REVERT: A 111 GLU cc_start: 0.7682 (tp30) cc_final: 0.7228 (tp30) REVERT: A 124 LYS cc_start: 0.7165 (ttpp) cc_final: 0.6608 (mtpp) REVERT: A 198 GLN cc_start: 0.7105 (tm-30) cc_final: 0.6489 (tm-30) REVERT: A 202 ASP cc_start: 0.7557 (m-30) cc_final: 0.6660 (m-30) REVERT: A 363 TYR cc_start: 0.6618 (t80) cc_final: 0.6259 (t80) outliers start: 11 outliers final: 11 residues processed: 120 average time/residue: 0.2370 time to fit residues: 33.2240 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 : 0.168 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 301 VAL 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 53 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4124 r_free = 0.4124 target = 0.151194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.136558 restraints weight = 21308.279| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.79 r_work: 0.3837 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4301 Z= 0.197 Angle : 0.568 10.116 5834 Z= 0.286 Chirality : 0.040 0.145 660 Planarity : 0.004 0.037 750 Dihedral : 4.228 16.404 607 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.26 % Allowed : 13.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.37), residues: 554 helix: 2.09 (0.36), residues: 227 sheet: -0.94 (0.45), residues: 130 loop : -0.50 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 182 TYR 0.010 0.002 TYR A 419 PHE 0.011 0.002 PHE A 26 TRP 0.005 0.001 TRP A 358 HIS 0.004 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 4295) covalent geometry : angle 0.54072 ( 5824) SS BOND : bond 0.00153 ( 2) SS BOND : angle 0.72948 ( 4) hydrogen bonds : bond 0.03838 ( 205) hydrogen bonds : angle 4.57570 ( 603) metal coordination : bond 0.00714 ( 4) metal coordination : angle 5.46959 ( 6) *********************** 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 130 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.213 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: 0.7102 (mtt) cc_final: 0.6710 (mtt) REVERT: K 108 GLU cc_start: 0.7669 (mp0) cc_final: 0.7026 (mp0) REVERT: A 111 GLU cc_start: 0.7647 (tp30) cc_final: 0.7209 (tp30) REVERT: A 124 LYS cc_start: 0.7195 (ttpp) cc_final: 0.6944 (mtpp) REVERT: A 202 ASP cc_start: 0.7484 (m-30) cc_final: 0.6810 (m-30) REVERT: A 363 TYR cc_start: 0.6700 (t80) cc_final: 0.6286 (t80) outliers start: 14 outliers final: 11 residues processed: 123 average time/residue: 0.2395 time to fit residues: 34.5605 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 : 0.221 ------------------------------------------------------------------------------- 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 120 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.150775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.136198 restraints weight = 21188.717| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.80 r_work: 0.3825 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4301 Z= 0.195 Angle : 0.564 10.112 5834 Z= 0.285 Chirality : 0.040 0.145 660 Planarity : 0.004 0.035 750 Dihedral : 4.308 16.976 607 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.20 % Allowed : 13.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.37), residues: 554 helix: 2.09 (0.36), residues: 228 sheet: -0.89 (0.45), residues: 130 loop : -0.61 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 267 TYR 0.011 0.002 TYR A 419 PHE 0.011 0.002 PHE A 26 TRP 0.007 0.001 TRP A 165 HIS 0.005 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 4295) covalent geometry : angle 0.53771 ( 5824) SS BOND : bond 0.00151 ( 2) SS BOND : angle 0.72790 ( 4) hydrogen bonds : bond 0.03837 ( 205) hydrogen bonds : angle 4.53261 ( 603) metal coordination : bond 0.00734 ( 4) metal coordination : angle 5.36307 ( 6) *********************** 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 132 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.232 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: 0.7179 (mtt) cc_final: 0.6836 (mtt) REVERT: K 108 GLU cc_start: 0.7676 (mp0) cc_final: 0.6976 (mp0) REVERT: A 73 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8171 (m) REVERT: A 111 GLU cc_start: 0.7639 (tp30) cc_final: 0.7202 (tp30) REVERT: A 202 ASP cc_start: 0.7340 (m-30) cc_final: 0.6903 (m-30) REVERT: A 363 TYR cc_start: 0.6730 (t80) cc_final: 0.6267 (t80) outliers start: 18 outliers final: 15 residues processed: 123 average time/residue: 0.2480 time to fit residues: 35.7221 Evaluate side-chains 122 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 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 K residue 110 GLU 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 59 SER Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 120 LYS 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 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 24 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 47 optimal weight: 0.2980 chunk 15 optimal weight: 0.3980 chunk 50 optimal weight: 0.0970 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 14 optimal weight: 0.0980 overall best weight: 0.2178 ------------------------------------------------------------------------------- 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 = 0.4135 r_free = 0.4135 target = 0.152119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.137543 restraints weight = 21408.618| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 2.82 r_work: 0.3849 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4301 Z= 0.113 Angle : 0.518 8.664 5834 Z= 0.261 Chirality : 0.039 0.149 660 Planarity : 0.004 0.031 750 Dihedral : 4.152 16.406 607 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.56 % Allowed : 14.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.37), residues: 554 helix: 2.29 (0.36), residues: 229 sheet: -0.82 (0.46), residues: 130 loop : -0.43 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 222 TYR 0.010 0.001 TYR A 419 PHE 0.009 0.001 PHE A 245 TRP 0.003 0.001 TRP A 358 HIS 0.002 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 4295) covalent geometry : angle 0.49773 ( 5824) SS BOND : bond 0.00257 ( 2) SS BOND : angle 0.94198 ( 4) hydrogen bonds : bond 0.03283 ( 205) hydrogen bonds : angle 4.30301 ( 603) metal coordination : bond 0.00397 ( 4) metal coordination : angle 4.45470 ( 6) *********************** 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 120 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.288 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: 0.6970 (mtt) cc_final: 0.6630 (mtt) REVERT: K 108 GLU cc_start: 0.7681 (mp0) cc_final: 0.7055 (mp0) REVERT: A 111 GLU cc_start: 0.7664 (tp30) cc_final: 0.7210 (tp30) REVERT: A 120 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7269 (pttm) REVERT: A 363 TYR cc_start: 0.6643 (t80) cc_final: 0.5971 (t80) REVERT: A 407 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7081 (mm-30) outliers start: 11 outliers final: 7 residues processed: 113 average time/residue: 0.2268 time to fit residues: 30.4639 Evaluate side-chains 114 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 120 LYS 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 25 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 30 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 198 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 = 0.150116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.135716 restraints weight = 21443.021| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.81 r_work: 0.3826 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4301 Z= 0.174 Angle : 0.559 9.800 5834 Z= 0.281 Chirality : 0.039 0.146 660 Planarity : 0.004 0.031 750 Dihedral : 4.143 15.896 607 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.37), residues: 554 helix: 2.26 (0.36), residues: 229 sheet: -0.95 (0.45), residues: 135 loop : -0.33 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG K 45 TYR 0.012 0.001 TYR A 419 PHE 0.010 0.002 PHE A 245 TRP 0.016 0.001 TRP A 165 HIS 0.004 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 4295) covalent geometry : angle 0.53398 ( 5824) SS BOND : bond 0.00140 ( 2) SS BOND : angle 1.14818 ( 4) hydrogen bonds : bond 0.03557 ( 205) hydrogen bonds : angle 4.33934 ( 603) metal coordination : bond 0.00651 ( 4) metal coordination : angle 5.14232 ( 6) *********************** 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 119 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.227 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: 0.7093 (mtt) cc_final: 0.6760 (mtt) REVERT: A 111 GLU cc_start: 0.7621 (tp30) cc_final: 0.7175 (tp30) REVERT: A 120 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7188 (pttm) REVERT: A 363 TYR cc_start: 0.6748 (t80) cc_final: 0.6056 (t80) REVERT: A 407 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7025 (mm-30) outliers start: 11 outliers final: 9 residues processed: 113 average time/residue: 0.2172 time to fit residues: 29.1852 Evaluate side-chains 116 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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 K residue 121 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 120 LYS 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 14 optimal weight: 0.7980 chunk 12 optimal weight: 0.0870 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.150449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.135567 restraints weight = 21423.795| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.90 r_work: 0.3823 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4301 Z= 0.152 Angle : 0.540 9.384 5834 Z= 0.272 Chirality : 0.039 0.147 660 Planarity : 0.004 0.030 750 Dihedral : 4.114 15.473 607 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.10 % Allowed : 15.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.37), residues: 554 helix: 2.30 (0.36), residues: 229 sheet: -0.86 (0.46), residues: 130 loop : -0.46 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 182 TYR 0.012 0.001 TYR K 111 PHE 0.010 0.001 PHE A 245 TRP 0.010 0.001 TRP A 165 HIS 0.003 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4295) covalent geometry : angle 0.51683 ( 5824) SS BOND : bond 0.00151 ( 2) SS BOND : angle 0.92365 ( 4) hydrogen bonds : bond 0.03363 ( 205) hydrogen bonds : angle 4.26650 ( 603) metal coordination : bond 0.00558 ( 4) metal coordination : angle 4.85063 ( 6) *********************** 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 118 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.221 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: 0.7055 (mtt) cc_final: 0.6745 (mtt) REVERT: K 108 GLU cc_start: 0.7694 (mp0) cc_final: 0.7035 (mp0) REVERT: A 111 GLU cc_start: 0.7696 (tp30) cc_final: 0.7237 (tp30) REVERT: A 120 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7173 (pttm) REVERT: A 363 TYR cc_start: 0.6765 (t80) cc_final: 0.6171 (t80) REVERT: A 407 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7172 (mm-30) outliers start: 9 outliers final: 6 residues processed: 114 average time/residue: 0.2092 time to fit residues: 28.2857 Evaluate side-chains 115 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 59 SER Chi-restraints excluded: chain A residue 120 LYS 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 38 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.0050 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.0870 chunk 47 optimal weight: 0.1980 chunk 43 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 overall best weight: 0.0950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.152876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.138153 restraints weight = 21253.460| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.88 r_work: 0.3859 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4301 Z= 0.098 Angle : 0.514 7.725 5834 Z= 0.257 Chirality : 0.039 0.151 660 Planarity : 0.004 0.039 750 Dihedral : 3.904 14.960 607 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.17 % Allowed : 16.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.37), residues: 554 helix: 2.52 (0.35), residues: 229 sheet: -0.92 (0.46), residues: 130 loop : -0.38 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 182 TYR 0.010 0.001 TYR K 111 PHE 0.007 0.001 PHE A 245 TRP 0.012 0.001 TRP A 165 HIS 0.003 0.001 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 4295) covalent geometry : angle 0.49654 ( 5824) SS BOND : bond 0.00230 ( 2) SS BOND : angle 0.69387 ( 4) hydrogen bonds : bond 0.02840 ( 205) hydrogen bonds : angle 4.00383 ( 603) metal coordination : bond 0.00311 ( 4) metal coordination : angle 4.14658 ( 6) ********************** 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 116 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.207 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: 0.6776 (mtt) cc_final: 0.6470 (mtt) REVERT: K 108 GLU cc_start: 0.7681 (mp0) cc_final: 0.7134 (mp0) REVERT: A 111 GLU cc_start: 0.7623 (tp30) cc_final: 0.7148 (tp30) REVERT: A 120 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7137 (pttm) REVERT: A 363 TYR cc_start: 0.6591 (t80) cc_final: 0.5995 (t80) REVERT: A 407 GLU cc_start: 0.7699 (mm-30) cc_final: 0.6871 (mm-30) outliers start: 5 outliers final: 4 residues processed: 113 average time/residue: 0.2214 time to fit residues: 29.4642 Evaluate side-chains 113 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 121 VAL Chi-restraints excluded: chain A residue 120 LYS 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: 1.9990 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.149002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.134462 restraints weight = 21314.691| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.82 r_work: 0.3807 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 4301 Z= 0.231 Angle : 0.596 10.479 5834 Z= 0.303 Chirality : 0.041 0.142 660 Planarity : 0.004 0.033 750 Dihedral : 4.180 14.940 607 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.40 % Allowed : 16.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.37), residues: 554 helix: 2.33 (0.35), residues: 229 sheet: -0.89 (0.46), residues: 125 loop : -0.65 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 182 TYR 0.012 0.002 TYR A 419 PHE 0.011 0.002 PHE A 26 TRP 0.007 0.001 TRP A 165 HIS 0.007 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 4295) covalent geometry : angle 0.56699 ( 5824) SS BOND : bond 0.00157 ( 2) SS BOND : angle 1.21289 ( 4) hydrogen bonds : bond 0.03809 ( 205) hydrogen bonds : angle 4.33018 ( 603) metal coordination : bond 0.00851 ( 4) metal coordination : angle 5.71498 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2606.87 seconds wall clock time: 44 minutes 58.05 seconds (2698.05 seconds total)