Starting phenix.real_space_refine on Fri Aug 22 17:38:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rl6_19332/08_2025/8rl6_19332.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rl6_19332/08_2025/8rl6_19332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rl6_19332/08_2025/8rl6_19332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rl6_19332/08_2025/8rl6_19332.map" model { file = "/net/cci-nas-00/data/ceres_data/8rl6_19332/08_2025/8rl6_19332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rl6_19332/08_2025/8rl6_19332.cif" } resolution = 3.18 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= 0.000 sd= 0.012 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 20 5.16 5 C 2083 2.51 5 N 575 2.21 5 O 597 1.98 5 H 3217 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6493 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6492 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 17, 'TRANS': 418} Chain breaks: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 7, 'GLN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 5, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 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 5920 SG CYS A 411 26.850 42.159 25.229 1.00 67.90 S ATOM 6155 SG CYS A 427 24.363 42.143 28.158 1.00 94.76 S ATOM 6204 SG CYS A 431 25.319 45.411 26.355 1.00 95.89 S ATOM 6243 SG CYS A 434 23.526 42.902 24.196 1.00 70.28 S Time building chain proxies: 1.51, per 1000 atoms: 0.23 Number of scatterers: 6493 At special positions: 0 Unit cell: (77.7, 81.9, 74.9, 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 20 16.00 O 597 8.00 N 575 7.00 C 2083 6.00 H 3217 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 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: 0.63 Conformation dependent library (CDL) restraints added in 271.1 milliseconds Enol-peptide restraints added in 238.4 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 431 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 434 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 427 " Number of angles added : 6 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 826 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 56.0% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 12 through 25 Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.629A pdb=" N CYS A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 79 through 93 Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 137 through 148 removed outlier: 4.452A pdb=" N THR A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 170 through 182 removed outlier: 4.039A pdb=" N GLY A 177 " --> pdb=" O TYR A 173 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 207 Processing helix chain 'A' and resid 237 through 251 removed outlier: 3.834A pdb=" N GLY A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 283 removed outlier: 3.596A pdb=" N GLU A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 307 Processing helix chain 'A' and resid 339 through 349 removed outlier: 3.929A pdb=" N ARG A 349 " --> pdb=" O GLN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 385 Processing helix chain 'A' and resid 388 through 407 removed outlier: 3.768A pdb=" N ILE A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 421 Processing helix chain 'A' and resid 436 through 451 removed outlier: 3.529A pdb=" N VAL A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.389A pdb=" N SER A 98 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N THR A 73 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE A 128 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL A 75 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE A 72 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL A 155 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE A 74 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N VAL A 189 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 154 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LEU A 191 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 156 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A 214 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 231 removed outlier: 5.801A pdb=" N PHE A 226 " --> pdb=" O CYS A 359 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU A 361 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP A 228 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N TYR A 363 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLN A 230 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL A 331 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N TYR A 362 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N HIS A 333 " --> pdb=" O TYR A 362 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A 263 " --> pdb=" O ALA A 332 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY A 262 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ALA A 315 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL A 264 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TYR A 289 " --> pdb=" O THR A 316 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 162 hydrogen bonds defined for protein. 477 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: 1.25 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3208 1.03 - 1.23: 10 1.23 - 1.42: 1369 1.42 - 1.62: 1944 1.62 - 1.81: 25 Bond restraints: 6556 Sorted by residual: bond pdb=" CG LEU A 176 " pdb=" CD1 LEU A 176 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.35e+00 bond pdb=" CB CYS A 427 " pdb=" HB2 CYS A 427 " ideal model delta sigma weight residual 0.970 0.954 0.016 2.00e-02 2.50e+03 6.46e-01 bond pdb=" N LEU A 176 " pdb=" CA LEU A 176 " ideal model delta sigma weight residual 1.457 1.467 -0.009 1.29e-02 6.01e+03 5.13e-01 bond pdb=" CB LEU A 183 " pdb=" CG LEU A 183 " ideal model delta sigma weight residual 1.530 1.543 -0.013 2.00e-02 2.50e+03 4.05e-01 bond pdb=" CB GLU A 407 " pdb=" CG GLU A 407 " ideal model delta sigma weight residual 1.520 1.502 0.018 3.00e-02 1.11e+03 3.68e-01 ... (remaining 6551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 11079 1.01 - 2.02: 717 2.02 - 3.03: 34 3.03 - 4.04: 12 4.04 - 5.06: 9 Bond angle restraints: 11851 Sorted by residual: angle pdb=" CB LEU A 279 " pdb=" CG LEU A 279 " pdb=" CD1 LEU A 279 " ideal model delta sigma weight residual 110.70 114.97 -4.27 3.00e+00 1.11e-01 2.03e+00 angle pdb=" CA LEU A 183 " pdb=" CB LEU A 183 " pdb=" CG LEU A 183 " ideal model delta sigma weight residual 116.30 120.89 -4.59 3.50e+00 8.16e-02 1.72e+00 angle pdb=" CB LEU A 176 " pdb=" CG LEU A 176 " pdb=" CD1 LEU A 176 " ideal model delta sigma weight residual 110.70 114.51 -3.81 3.00e+00 1.11e-01 1.61e+00 angle pdb=" CA TYR A 173 " pdb=" CB TYR A 173 " pdb=" CG TYR A 173 " ideal model delta sigma weight residual 113.90 111.64 2.26 1.80e+00 3.09e-01 1.57e+00 angle pdb=" CB MET A 132 " pdb=" CG MET A 132 " pdb=" SD MET A 132 " ideal model delta sigma weight residual 112.70 116.43 -3.73 3.00e+00 1.11e-01 1.55e+00 ... (remaining 11846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.53: 2784 15.53 - 31.06: 224 31.06 - 46.59: 56 46.59 - 62.11: 30 62.11 - 77.64: 8 Dihedral angle restraints: 3102 sinusoidal: 1636 harmonic: 1466 Sorted by residual: 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 55.80 37.20 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CA TYR A 363 " pdb=" C TYR A 363 " pdb=" N SER A 364 " pdb=" CA SER A 364 " ideal model delta harmonic sigma weight residual 180.00 163.55 16.45 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CG ARG A 412 " pdb=" CD ARG A 412 " pdb=" NE ARG A 412 " pdb=" CZ ARG A 412 " ideal model delta sinusoidal sigma weight residual -90.00 -49.78 -40.22 2 1.50e+01 4.44e-03 8.90e+00 ... (remaining 3099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 332 0.024 - 0.047: 102 0.047 - 0.071: 49 0.071 - 0.094: 21 0.094 - 0.118: 21 Chirality restraints: 525 Sorted by residual: 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 2.56 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA ILE A 128 " pdb=" N ILE A 128 " pdb=" C ILE A 128 " pdb=" CB ILE A 128 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 chirality pdb=" CA ILE A 74 " pdb=" N ILE A 74 " pdb=" C ILE A 74 " pdb=" CB ILE A 74 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 ... (remaining 522 not shown) Planarity restraints: 996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 363 " 0.013 2.00e-02 2.50e+03 9.54e-03 2.73e+00 pdb=" CG TYR A 363 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 363 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 363 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 363 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 363 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 363 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 363 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TYR A 363 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR A 363 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR A 363 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR A 363 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 412 " -0.128 9.50e-02 1.11e+02 4.29e-02 2.17e+00 pdb=" NE ARG A 412 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 412 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 412 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 412 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 412 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 412 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 412 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 412 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 196 " -0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO A 197 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 197 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 197 " -0.016 5.00e-02 4.00e+02 ... (remaining 993 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 600 2.22 - 2.81: 14437 2.81 - 3.41: 18983 3.41 - 4.00: 24217 4.00 - 4.60: 37030 Nonbonded interactions: 95267 Sorted by model distance: nonbonded pdb=" O ASP A 157 " pdb=" HH TYR A 173 " model vdw 1.621 2.450 nonbonded pdb=" H ALA A 159 " pdb=" O LEU A 191 " model vdw 1.652 2.450 nonbonded pdb=" HE2 HIS A 333 " pdb=" OE1 GLU A 346 " model vdw 1.666 2.450 nonbonded pdb=" O ARG A 175 " pdb=" H ALA A 178 " model vdw 1.681 2.450 nonbonded pdb=" O LEU A 382 " pdb=" H GLY A 387 " model vdw 1.739 2.450 ... (remaining 95262 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 5.020 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.620 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 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 : 0.003 0.038 3344 Z= 0.113 Angle : 0.552 12.648 4537 Z= 0.254 Chirality : 0.037 0.118 525 Planarity : 0.004 0.056 580 Dihedral : 13.535 77.642 1194 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.86 (0.43), residues: 432 helix: 2.14 (0.35), residues: 226 sheet: -0.90 (0.62), residues: 74 loop : 1.17 (0.61), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 349 TYR 0.027 0.002 TYR A 363 PHE 0.009 0.001 PHE A 216 TRP 0.003 0.001 TRP A 334 HIS 0.003 0.001 HIS A 433 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 3339) covalent geometry : angle 0.49378 ( 4529) SS BOND : bond 0.00247 ( 1) SS BOND : angle 0.78293 ( 2) hydrogen bonds : bond 0.12246 ( 162) hydrogen bonds : angle 6.06628 ( 477) metal coordination : bond 0.01832 ( 4) metal coordination : angle 6.81760 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue SER 259 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue LYS 338 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 VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.180 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: A 359 CYS cc_start: 0.6830 (m) cc_final: 0.6625 (m) REVERT: A 407 GLU cc_start: 0.6589 (mp0) cc_final: 0.6322 (mp0) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1261 time to fit residues: 12.9389 Evaluate side-chains 78 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.206364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.186831 restraints weight = 15692.866| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 3.29 r_work: 0.4256 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 3344 Z= 0.257 Angle : 0.667 11.859 4537 Z= 0.338 Chirality : 0.040 0.143 525 Planarity : 0.005 0.049 580 Dihedral : 4.280 14.955 469 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.90 % Allowed : 8.11 % Favored : 90.99 % 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: 0.92 (0.42), residues: 432 helix: 1.55 (0.35), residues: 228 sheet: -1.98 (0.55), residues: 75 loop : 0.86 (0.59), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 412 TYR 0.024 0.002 TYR A 363 PHE 0.021 0.002 PHE A 49 TRP 0.009 0.002 TRP A 305 HIS 0.008 0.002 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 3339) covalent geometry : angle 0.61895 ( 4529) SS BOND : bond 0.00409 ( 1) SS BOND : angle 0.49295 ( 2) hydrogen bonds : bond 0.04221 ( 162) hydrogen bonds : angle 5.15142 ( 477) metal coordination : bond 0.01481 ( 4) metal coordination : angle 6.86803 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue SER 259 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue LYS 338 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 VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6673 (mm-40) cc_final: 0.6409 (mm-40) REVERT: A 151 LEU cc_start: 0.7822 (tp) cc_final: 0.7575 (tt) REVERT: A 248 LYS cc_start: 0.7798 (tppt) cc_final: 0.7456 (mmmt) REVERT: A 407 GLU cc_start: 0.6860 (mp0) cc_final: 0.6577 (mp0) outliers start: 3 outliers final: 3 residues processed: 76 average time/residue: 0.1234 time to fit residues: 12.1028 Evaluate side-chains 77 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 364 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.0670 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 40 optimal weight: 0.6980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.205820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.186120 restraints weight = 15639.008| |-----------------------------------------------------------------------------| r_work (start): 0.4393 rms_B_bonded: 3.30 r_work: 0.4265 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3344 Z= 0.170 Angle : 0.558 9.513 4537 Z= 0.273 Chirality : 0.037 0.127 525 Planarity : 0.004 0.042 580 Dihedral : 4.170 16.213 469 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.60 % Allowed : 9.61 % Favored : 89.79 % 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: 0.90 (0.42), residues: 432 helix: 1.49 (0.35), residues: 228 sheet: -2.03 (0.55), residues: 75 loop : 0.97 (0.59), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 329 TYR 0.027 0.002 TYR A 363 PHE 0.012 0.002 PHE A 49 TRP 0.007 0.001 TRP A 305 HIS 0.004 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 3339) covalent geometry : angle 0.51217 ( 4529) SS BOND : bond 0.00458 ( 1) SS BOND : angle 0.53285 ( 2) hydrogen bonds : bond 0.03741 ( 162) hydrogen bonds : angle 4.96456 ( 477) metal coordination : bond 0.01138 ( 4) metal coordination : angle 6.12368 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue SER 259 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue LYS 338 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 VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6643 (mm-40) cc_final: 0.6383 (mm-40) REVERT: A 346 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6996 (mt-10) outliers start: 2 outliers final: 2 residues processed: 75 average time/residue: 0.1104 time to fit residues: 10.7883 Evaluate side-chains 73 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.201608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.181484 restraints weight = 15696.170| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 3.33 r_work: 0.4193 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 3344 Z= 0.281 Angle : 0.670 11.310 4537 Z= 0.344 Chirality : 0.040 0.121 525 Planarity : 0.006 0.060 580 Dihedral : 4.767 16.114 469 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.80 % Allowed : 10.21 % Favored : 87.99 % 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: 0.16 (0.41), residues: 432 helix: 0.96 (0.36), residues: 222 sheet: -2.19 (0.56), residues: 75 loop : 0.39 (0.55), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 329 TYR 0.019 0.002 TYR A 363 PHE 0.022 0.002 PHE A 49 TRP 0.014 0.002 TRP A 305 HIS 0.009 0.003 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00575 ( 3339) covalent geometry : angle 0.62844 ( 4529) SS BOND : bond 0.00663 ( 1) SS BOND : angle 1.03296 ( 2) hydrogen bonds : bond 0.04559 ( 162) hydrogen bonds : angle 5.30139 ( 477) metal coordination : bond 0.01483 ( 4) metal coordination : angle 6.37052 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue SER 259 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue LYS 338 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 VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6701 (mm-40) cc_final: 0.6442 (mm-40) REVERT: A 180 ARG cc_start: 0.6794 (tpt90) cc_final: 0.6029 (tpt90) REVERT: A 189 VAL cc_start: 0.8368 (t) cc_final: 0.7787 (m) REVERT: A 345 GLN cc_start: 0.7237 (mm110) cc_final: 0.6470 (mm110) REVERT: A 346 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6814 (mt-10) outliers start: 6 outliers final: 4 residues processed: 80 average time/residue: 0.1144 time to fit residues: 11.8228 Evaluate side-chains 80 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.201296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.181093 restraints weight = 15576.509| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 3.33 r_work: 0.4202 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3344 Z= 0.220 Angle : 0.614 10.536 4537 Z= 0.304 Chirality : 0.038 0.122 525 Planarity : 0.005 0.050 580 Dihedral : 4.635 16.501 469 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.80 % Allowed : 12.01 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.07 (0.42), residues: 432 helix: 0.87 (0.35), residues: 225 sheet: -2.24 (0.57), residues: 74 loop : 0.37 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 329 TYR 0.014 0.002 TYR A 363 PHE 0.025 0.002 PHE A 399 TRP 0.012 0.002 TRP A 305 HIS 0.005 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 3339) covalent geometry : angle 0.55894 ( 4529) SS BOND : bond 0.00506 ( 1) SS BOND : angle 1.15979 ( 2) hydrogen bonds : bond 0.04024 ( 162) hydrogen bonds : angle 5.09169 ( 477) metal coordination : bond 0.01554 ( 4) metal coordination : angle 6.98567 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue SER 259 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue LYS 338 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 VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6637 (mm-40) cc_final: 0.6422 (mm-40) REVERT: A 164 GLN cc_start: 0.7903 (mt0) cc_final: 0.7674 (mt0) REVERT: A 180 ARG cc_start: 0.6734 (tpt90) cc_final: 0.6051 (tpt90) REVERT: A 345 GLN cc_start: 0.7245 (mm110) cc_final: 0.6505 (mm110) REVERT: A 346 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6792 (mt-10) outliers start: 6 outliers final: 6 residues processed: 80 average time/residue: 0.0995 time to fit residues: 10.2455 Evaluate side-chains 83 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4521 r_free = 0.4521 target = 0.199084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.178519 restraints weight = 15293.357| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 3.37 r_work: 0.4171 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3344 Z= 0.261 Angle : 0.652 9.827 4537 Z= 0.331 Chirality : 0.039 0.121 525 Planarity : 0.005 0.051 580 Dihedral : 4.916 17.599 469 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.40 % Allowed : 12.31 % Favored : 85.29 % 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: -0.19 (0.42), residues: 432 helix: 0.68 (0.35), residues: 225 sheet: -2.31 (0.60), residues: 66 loop : -0.02 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 329 TYR 0.016 0.002 TYR A 363 PHE 0.025 0.002 PHE A 399 TRP 0.015 0.002 TRP A 305 HIS 0.006 0.002 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00534 ( 3339) covalent geometry : angle 0.60154 ( 4529) SS BOND : bond 0.00520 ( 1) SS BOND : angle 1.35310 ( 2) hydrogen bonds : bond 0.04308 ( 162) hydrogen bonds : angle 5.33771 ( 477) metal coordination : bond 0.01565 ( 4) metal coordination : angle 6.90544 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue SER 259 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue LYS 338 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 VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7514 (mp) REVERT: A 180 ARG cc_start: 0.6808 (tpt90) cc_final: 0.6184 (tpt90) REVERT: A 204 PHE cc_start: 0.7873 (m-80) cc_final: 0.7580 (m-80) REVERT: A 345 GLN cc_start: 0.7243 (mm110) cc_final: 0.6540 (mm110) REVERT: A 346 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6791 (mt-10) outliers start: 8 outliers final: 4 residues processed: 80 average time/residue: 0.0991 time to fit residues: 10.1471 Evaluate side-chains 81 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 285 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 11 optimal weight: 0.0980 chunk 3 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.0770 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.201184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.180541 restraints weight = 15048.899| |-----------------------------------------------------------------------------| r_work (start): 0.4315 rms_B_bonded: 3.36 r_work: 0.4198 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3344 Z= 0.162 Angle : 0.578 8.744 4537 Z= 0.288 Chirality : 0.038 0.129 525 Planarity : 0.004 0.039 580 Dihedral : 4.610 17.234 469 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.10 % Allowed : 14.11 % Favored : 83.78 % 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: 0.02 (0.43), residues: 432 helix: 0.72 (0.35), residues: 225 sheet: -2.18 (0.57), residues: 75 loop : 0.52 (0.63), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 329 TYR 0.018 0.002 TYR A 363 PHE 0.031 0.002 PHE A 399 TRP 0.010 0.001 TRP A 305 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 3339) covalent geometry : angle 0.53906 ( 4529) SS BOND : bond 0.00375 ( 1) SS BOND : angle 1.08440 ( 2) hydrogen bonds : bond 0.03723 ( 162) hydrogen bonds : angle 4.97032 ( 477) metal coordination : bond 0.01103 ( 4) metal coordination : angle 5.70708 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue SER 259 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue LYS 338 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 VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.167 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: A 72 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7518 (mp) REVERT: A 180 ARG cc_start: 0.6682 (tpt90) cc_final: 0.6087 (tpt90) REVERT: A 345 GLN cc_start: 0.7208 (mm110) cc_final: 0.6536 (mm110) REVERT: A 346 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6881 (mt-10) REVERT: A 363 TYR cc_start: 0.5994 (t80) cc_final: 0.5459 (t80) REVERT: A 407 GLU cc_start: 0.6690 (mp0) cc_final: 0.6316 (mp0) outliers start: 7 outliers final: 5 residues processed: 79 average time/residue: 0.1241 time to fit residues: 12.4995 Evaluate side-chains 82 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 285 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 0.0770 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 0.0970 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.201687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.180861 restraints weight = 15267.476| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 3.42 r_work: 0.4202 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3344 Z= 0.147 Angle : 0.569 8.577 4537 Z= 0.284 Chirality : 0.037 0.126 525 Planarity : 0.004 0.038 580 Dihedral : 4.492 16.917 469 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.50 % Allowed : 15.02 % Favored : 83.48 % 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: 0.06 (0.43), residues: 432 helix: 0.77 (0.35), residues: 227 sheet: -2.16 (0.57), residues: 75 loop : 0.50 (0.64), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 329 TYR 0.018 0.002 TYR A 363 PHE 0.031 0.002 PHE A 399 TRP 0.009 0.001 TRP A 305 HIS 0.002 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3339) covalent geometry : angle 0.53521 ( 4529) SS BOND : bond 0.00382 ( 1) SS BOND : angle 1.09049 ( 2) hydrogen bonds : bond 0.03526 ( 162) hydrogen bonds : angle 4.87518 ( 477) metal coordination : bond 0.01027 ( 4) metal coordination : angle 5.32345 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue SER 259 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue LYS 338 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 VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.131 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: A 72 ILE cc_start: 0.7903 (pt) cc_final: 0.7514 (mp) REVERT: A 180 ARG cc_start: 0.6662 (tpt90) cc_final: 0.6045 (tpt90) REVERT: A 345 GLN cc_start: 0.7212 (mm110) cc_final: 0.6538 (mm110) REVERT: A 346 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6795 (mt-10) outliers start: 5 outliers final: 5 residues processed: 78 average time/residue: 0.1130 time to fit residues: 11.4064 Evaluate side-chains 80 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 405 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 26 optimal weight: 0.5980 chunk 11 optimal weight: 0.0970 chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.200584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.179600 restraints weight = 15108.889| |-----------------------------------------------------------------------------| r_work (start): 0.4311 rms_B_bonded: 3.43 r_work: 0.4188 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3344 Z= 0.180 Angle : 0.582 8.796 4537 Z= 0.294 Chirality : 0.037 0.125 525 Planarity : 0.004 0.037 580 Dihedral : 4.574 17.001 469 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.10 % Allowed : 14.41 % Favored : 83.48 % 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: 0.05 (0.42), residues: 432 helix: 0.79 (0.35), residues: 225 sheet: -2.20 (0.57), residues: 76 loop : 0.50 (0.62), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 329 TYR 0.016 0.002 TYR A 363 PHE 0.026 0.002 PHE A 399 TRP 0.011 0.001 TRP A 305 HIS 0.006 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 3339) covalent geometry : angle 0.54744 ( 4529) SS BOND : bond 0.00429 ( 1) SS BOND : angle 1.10304 ( 2) hydrogen bonds : bond 0.03667 ( 162) hydrogen bonds : angle 4.90207 ( 477) metal coordination : bond 0.01129 ( 4) metal coordination : angle 5.44715 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue SER 259 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue LYS 338 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 VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.179 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: A 72 ILE cc_start: 0.7902 (pt) cc_final: 0.7565 (mp) REVERT: A 180 ARG cc_start: 0.6662 (tpt90) cc_final: 0.6037 (tpt90) REVERT: A 345 GLN cc_start: 0.7219 (mm110) cc_final: 0.6520 (mm110) REVERT: A 346 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6959 (mt-10) outliers start: 7 outliers final: 6 residues processed: 81 average time/residue: 0.1136 time to fit residues: 11.7389 Evaluate side-chains 83 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 405 PHE Chi-restraints excluded: chain A residue 407 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 35 optimal weight: 0.2980 chunk 20 optimal weight: 0.0000 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 15 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.201387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.180521 restraints weight = 15075.752| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 3.46 r_work: 0.4194 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3344 Z= 0.143 Angle : 0.594 13.014 4537 Z= 0.280 Chirality : 0.037 0.125 525 Planarity : 0.004 0.034 580 Dihedral : 4.442 16.354 469 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.20 % Allowed : 15.62 % Favored : 83.18 % 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: 0.15 (0.42), residues: 432 helix: 0.83 (0.34), residues: 227 sheet: -2.04 (0.61), residues: 67 loop : 0.32 (0.60), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 329 TYR 0.015 0.002 TYR A 363 PHE 0.020 0.002 PHE A 399 TRP 0.008 0.001 TRP A 305 HIS 0.002 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3339) covalent geometry : angle 0.52534 ( 4529) SS BOND : bond 0.00348 ( 1) SS BOND : angle 0.99665 ( 2) hydrogen bonds : bond 0.03383 ( 162) hydrogen bonds : angle 4.75839 ( 477) metal coordination : bond 0.01385 ( 4) metal coordination : angle 7.60862 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue SER 259 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue LYS 338 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 VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.171 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: A 72 ILE cc_start: 0.7934 (pt) cc_final: 0.7596 (mp) REVERT: A 180 ARG cc_start: 0.6633 (tpt90) cc_final: 0.6039 (tpt90) REVERT: A 345 GLN cc_start: 0.7176 (mm110) cc_final: 0.6490 (mm110) REVERT: A 346 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6722 (mt-10) outliers start: 4 outliers final: 4 residues processed: 79 average time/residue: 0.1128 time to fit residues: 11.4885 Evaluate side-chains 80 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 405 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 37 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 36 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.199563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.178510 restraints weight = 15161.694| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 3.47 r_work: 0.4179 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3344 Z= 0.183 Angle : 0.620 12.030 4537 Z= 0.299 Chirality : 0.038 0.135 525 Planarity : 0.004 0.035 580 Dihedral : 4.555 16.273 469 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.80 % Allowed : 15.32 % Favored : 82.88 % 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: 0.21 (0.42), residues: 432 helix: 0.83 (0.34), residues: 225 sheet: -1.97 (0.62), residues: 67 loop : 0.43 (0.60), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 329 TYR 0.013 0.002 TYR A 363 PHE 0.021 0.002 PHE A 204 TRP 0.011 0.001 TRP A 305 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 3339) covalent geometry : angle 0.55295 ( 4529) SS BOND : bond 0.00443 ( 1) SS BOND : angle 1.00552 ( 2) hydrogen bonds : bond 0.03618 ( 162) hydrogen bonds : angle 4.84888 ( 477) metal coordination : bond 0.01885 ( 4) metal coordination : angle 7.70372 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2389.92 seconds wall clock time: 41 minutes 13.33 seconds (2473.33 seconds total)