Starting phenix.real_space_refine on Tue Mar 11 18:53:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rl6_19332/03_2025/8rl6_19332.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rl6_19332/03_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_19332/03_2025/8rl6_19332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rl6_19332/03_2025/8rl6_19332.map" model { file = "/net/cci-nas-00/data/ceres_data/8rl6_19332/03_2025/8rl6_19332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rl6_19332/03_2025/8rl6_19332.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 7} 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: 5.17, per 1000 atoms: 0.80 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: 1.69 Conformation dependent library (CDL) restraints added in 665.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 411 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 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: 0.57 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: 2.25 Time building geometry restraints manager: 2.06 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: 6.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.770 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.100 ------------------------------------------------------------------------------- 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 : 0.002 0.038 3339 Z= 0.163 Angle : 0.494 5.055 4529 Z= 0.250 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (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 TRP 0.003 0.001 TRP A 334 HIS 0.003 0.001 HIS A 433 PHE 0.009 0.001 PHE A 216 TYR 0.027 0.002 TYR A 363 ARG 0.007 0.001 ARG A 349 *********************** 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 : 0.488 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: A 359 CYS cc_start: 0.6830 (m) cc_final: 0.6624 (m) REVERT: A 407 GLU cc_start: 0.6589 (mp0) cc_final: 0.6319 (mp0) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2826 time to fit residues: 28.7638 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 : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.4612 r_free = 0.4612 target = 0.208280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.188656 restraints weight = 15732.714| |-----------------------------------------------------------------------------| r_work (start): 0.4402 rms_B_bonded: 3.23 r_work: 0.4276 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3339 Z= 0.315 Angle : 0.586 5.680 4529 Z= 0.315 Chirality : 0.039 0.138 525 Planarity : 0.005 0.043 580 Dihedral : 4.136 14.929 469 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.60 % Allowed : 8.11 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.42), residues: 432 helix: 1.72 (0.35), residues: 228 sheet: -1.90 (0.55), residues: 75 loop : 0.91 (0.59), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 305 HIS 0.006 0.002 HIS A 89 PHE 0.019 0.002 PHE A 49 TYR 0.025 0.002 TYR A 363 ARG 0.004 0.001 ARG A 412 *********************** 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: 2 poor density : 76 time to evaluate : 0.523 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: 0.6613 (mm-40) cc_final: 0.6356 (mm-40) REVERT: A 151 LEU cc_start: 0.7772 (tp) cc_final: 0.7510 (tt) REVERT: A 407 GLU cc_start: 0.6819 (mp0) cc_final: 0.6520 (mp0) outliers start: 2 outliers final: 2 residues processed: 77 average time/residue: 0.2823 time to fit residues: 27.5961 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 : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4572 r_free = 0.4572 target = 0.204904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.184357 restraints weight = 15706.527| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 3.41 r_work: 0.4225 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 3339 Z= 0.313 Angle : 0.576 6.390 4529 Z= 0.308 Chirality : 0.039 0.133 525 Planarity : 0.005 0.051 580 Dihedral : 4.478 16.715 469 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.10 % Allowed : 9.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.42), residues: 432 helix: 1.25 (0.35), residues: 227 sheet: -2.14 (0.53), residues: 75 loop : 0.79 (0.59), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 305 HIS 0.006 0.002 HIS A 89 PHE 0.018 0.002 PHE A 49 TYR 0.030 0.002 TYR A 363 ARG 0.005 0.001 ARG A 442 *********************** 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 81 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6693 (mm-40) cc_final: 0.6447 (mm-40) REVERT: A 189 VAL cc_start: 0.8342 (t) cc_final: 0.7840 (m) REVERT: A 346 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7104 (mt-10) outliers start: 7 outliers final: 6 residues processed: 77 average time/residue: 0.2675 time to fit residues: 26.6505 Evaluate side-chains 78 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 183 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 19 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 0.0980 overall best weight: 0.2378 ------------------------------------------------------------------------------- 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 = 0.4595 r_free = 0.4595 target = 0.207013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.186240 restraints weight = 15901.964| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 3.47 r_work: 0.4250 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3339 Z= 0.175 Angle : 0.487 5.760 4529 Z= 0.250 Chirality : 0.037 0.129 525 Planarity : 0.004 0.036 580 Dihedral : 4.104 16.294 469 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.60 % Allowed : 12.01 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.43), residues: 432 helix: 1.38 (0.35), residues: 228 sheet: -2.10 (0.55), residues: 74 loop : 1.03 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 305 HIS 0.002 0.001 HIS A 208 PHE 0.012 0.001 PHE A 204 TYR 0.013 0.001 TYR A 363 ARG 0.003 0.000 ARG A 329 *********************** 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 75 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6617 (mm-40) cc_final: 0.6380 (mm-40) REVERT: A 180 ARG cc_start: 0.6647 (tpt90) cc_final: 0.6176 (tpt90) REVERT: A 346 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6941 (mt-10) outliers start: 2 outliers final: 2 residues processed: 74 average time/residue: 0.2525 time to fit residues: 24.1414 Evaluate side-chains 75 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 444 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 11 optimal weight: 0.0170 chunk 17 optimal weight: 0.0570 chunk 16 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.3536 ------------------------------------------------------------------------------- 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 = 0.4579 r_free = 0.4579 target = 0.205513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.184991 restraints weight = 15819.818| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 3.41 r_work: 0.4232 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6125 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3339 Z= 0.219 Angle : 0.506 5.746 4529 Z= 0.264 Chirality : 0.037 0.121 525 Planarity : 0.004 0.035 580 Dihedral : 4.103 16.343 469 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.10 % Allowed : 12.31 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.42), residues: 432 helix: 1.40 (0.35), residues: 227 sheet: -2.11 (0.56), residues: 74 loop : 0.89 (0.58), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 305 HIS 0.008 0.002 HIS A 290 PHE 0.015 0.002 PHE A 204 TYR 0.012 0.001 TYR A 363 ARG 0.003 0.000 ARG A 329 *********************** 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 79 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6583 (mm-40) cc_final: 0.6381 (mm-40) REVERT: A 346 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6832 (mt-10) outliers start: 7 outliers final: 5 residues processed: 75 average time/residue: 0.2526 time to fit residues: 24.5449 Evaluate side-chains 76 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 285 ASN Chi-restraints excluded: chain A residue 444 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 26 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 0.2780 ------------------------------------------------------------------------------- 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 = 0.4579 r_free = 0.4579 target = 0.205689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.185411 restraints weight = 15544.602| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 3.39 r_work: 0.4241 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3339 Z= 0.185 Angle : 0.493 5.503 4529 Z= 0.254 Chirality : 0.037 0.123 525 Planarity : 0.004 0.034 580 Dihedral : 4.037 15.971 469 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.80 % Allowed : 12.31 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.43), residues: 432 helix: 1.49 (0.35), residues: 227 sheet: -2.01 (0.56), residues: 75 loop : 0.97 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 305 HIS 0.006 0.001 HIS A 290 PHE 0.016 0.001 PHE A 204 TYR 0.009 0.001 TYR A 173 ARG 0.002 0.000 ARG A 329 *********************** 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 74 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6593 (mm-40) cc_final: 0.6392 (mm-40) REVERT: A 204 PHE cc_start: 0.7926 (m-80) cc_final: 0.7503 (m-80) REVERT: A 346 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6796 (mt-10) REVERT: A 363 TYR cc_start: 0.5780 (t80) cc_final: 0.5302 (t80) REVERT: A 407 GLU cc_start: 0.6553 (mp0) cc_final: 0.6276 (mp0) outliers start: 6 outliers final: 6 residues processed: 71 average time/residue: 0.2593 time to fit residues: 23.7601 Evaluate side-chains 73 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4534 r_free = 0.4534 target = 0.199935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.179843 restraints weight = 15477.851| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 3.30 r_work: 0.4197 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3339 Z= 0.350 Angle : 0.594 6.003 4529 Z= 0.321 Chirality : 0.039 0.122 525 Planarity : 0.005 0.047 580 Dihedral : 4.660 16.255 469 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.10 % Allowed : 12.91 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.43), residues: 432 helix: 1.03 (0.35), residues: 225 sheet: -2.21 (0.57), residues: 75 loop : 0.62 (0.60), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 305 HIS 0.008 0.002 HIS A 208 PHE 0.018 0.002 PHE A 49 TYR 0.014 0.002 TYR A 363 ARG 0.004 0.001 ARG A 329 *********************** 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 81 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7486 (mp) REVERT: A 345 GLN cc_start: 0.7235 (mm110) cc_final: 0.6566 (mm110) outliers start: 7 outliers final: 5 residues processed: 78 average time/residue: 0.2577 time to fit residues: 26.1654 Evaluate side-chains 79 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 183 LEU 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 38 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 42 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 31 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 0.0980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 overall best weight: 0.2580 ------------------------------------------------------------------------------- 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** A 185 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.202327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.181574 restraints weight = 15169.620| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 3.38 r_work: 0.4213 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3339 Z= 0.192 Angle : 0.517 5.427 4529 Z= 0.269 Chirality : 0.038 0.126 525 Planarity : 0.004 0.035 580 Dihedral : 4.273 16.554 469 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.50 % Allowed : 13.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.43), residues: 432 helix: 1.14 (0.35), residues: 227 sheet: -2.18 (0.56), residues: 75 loop : 0.74 (0.62), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 305 HIS 0.004 0.001 HIS A 290 PHE 0.018 0.002 PHE A 204 TYR 0.009 0.001 TYR A 344 ARG 0.004 0.000 ARG A 329 *********************** 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 : 0.459 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: A 204 PHE cc_start: 0.7897 (m-80) cc_final: 0.7643 (m-80) outliers start: 5 outliers final: 5 residues processed: 79 average time/residue: 0.2491 time to fit residues: 25.3217 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 : 0.614 ------------------------------------------------------------------------------- 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 185 HIS Chi-restraints excluded: chain A residue 202 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 6 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 0.0970 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 0.0970 chunk 41 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 overall best weight: 0.2376 ------------------------------------------------------------------------------- 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 = 0.4563 r_free = 0.4563 target = 0.202932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.182054 restraints weight = 15243.832| |-----------------------------------------------------------------------------| r_work (start): 0.4331 rms_B_bonded: 3.42 r_work: 0.4215 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3339 Z= 0.195 Angle : 0.520 5.486 4529 Z= 0.270 Chirality : 0.038 0.127 525 Planarity : 0.004 0.035 580 Dihedral : 4.217 16.733 469 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.20 % Allowed : 15.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.43), residues: 432 helix: 1.14 (0.34), residues: 227 sheet: -2.03 (0.62), residues: 66 loop : 0.74 (0.62), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 305 HIS 0.004 0.001 HIS A 290 PHE 0.015 0.001 PHE A 204 TYR 0.016 0.002 TYR A 363 ARG 0.003 0.000 ARG A 329 *********************** 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 78 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.7837 (pt) cc_final: 0.7310 (mp) REVERT: A 248 LYS cc_start: 0.7883 (tppt) cc_final: 0.7657 (tppt) REVERT: A 363 TYR cc_start: 0.5943 (t80) cc_final: 0.5416 (t80) REVERT: A 407 GLU cc_start: 0.6932 (mp0) cc_final: 0.6552 (mp0) outliers start: 4 outliers final: 4 residues processed: 77 average time/residue: 0.2749 time to fit residues: 26.7418 Evaluate side-chains 77 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 15 optimal weight: 0.0870 chunk 25 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 12 optimal weight: 0.0670 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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** A 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.201355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.180360 restraints weight = 15169.826| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 3.41 r_work: 0.4198 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3339 Z= 0.240 Angle : 0.558 6.071 4529 Z= 0.290 Chirality : 0.038 0.125 525 Planarity : 0.004 0.036 580 Dihedral : 4.332 16.347 469 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.50 % Allowed : 16.82 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.43), residues: 432 helix: 1.03 (0.34), residues: 227 sheet: -2.08 (0.60), residues: 67 loop : 0.61 (0.61), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 305 HIS 0.006 0.002 HIS A 185 PHE 0.025 0.002 PHE A 204 TYR 0.016 0.002 TYR A 363 ARG 0.004 0.000 ARG A 329 ********************** 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 79 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ILE cc_start: 0.7904 (pt) cc_final: 0.7369 (mp) outliers start: 5 outliers final: 5 residues processed: 78 average time/residue: 0.2642 time to fit residues: 26.2263 Evaluate side-chains 79 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 163 SER Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 202 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 37 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 17 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.4551 r_free = 0.4551 target = 0.201607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.180665 restraints weight = 15329.587| |-----------------------------------------------------------------------------| r_work (start): 0.4319 rms_B_bonded: 3.44 r_work: 0.4196 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3339 Z= 0.235 Angle : 0.550 5.567 4529 Z= 0.288 Chirality : 0.038 0.135 525 Planarity : 0.004 0.035 580 Dihedral : 4.393 16.393 469 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.80 % Allowed : 16.52 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.43), residues: 432 helix: 1.05 (0.34), residues: 227 sheet: -2.05 (0.60), residues: 67 loop : 0.71 (0.61), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 305 HIS 0.005 0.002 HIS A 185 PHE 0.022 0.002 PHE A 204 TYR 0.019 0.002 TYR A 363 ARG 0.003 0.000 ARG A 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5352.49 seconds wall clock time: 91 minutes 12.21 seconds (5472.21 seconds total)