Starting phenix.real_space_refine on Tue Feb 11 19:24:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rl6_19332/02_2025/8rl6_19332.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rl6_19332/02_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_19332/02_2025/8rl6_19332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rl6_19332/02_2025/8rl6_19332.map" model { file = "/net/cci-nas-00/data/ceres_data/8rl6_19332/02_2025/8rl6_19332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rl6_19332/02_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-5592/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: 4.86, per 1000 atoms: 0.75 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: 1.58 Conformation dependent library (CDL) restraints added in 598.7 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: 0.47 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: 2.42 Time building geometry restraints manager: 1.90 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: 4.080 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.720 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.950 ------------------------------------------------------------------------------- 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 : 0.453 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: 0.2790 time to fit residues: 28.3047 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 : 0.431 ------------------------------------------------------------------------------- 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: 0.7980 chunk 25 optimal weight: 0.5980 chunk 39 optimal weight: 0.0980 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 = 0.4631 r_free = 0.4631 target = 0.209350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.190025 restraints weight = 15806.558| |-----------------------------------------------------------------------------| r_work (start): 0.4428 rms_B_bonded: 3.23 r_work: 0.4311 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3339 Z= 0.253 Angle : 0.542 5.281 4529 Z= 0.287 Chirality : 0.039 0.135 525 Planarity : 0.004 0.033 580 Dihedral : 3.949 14.943 469 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.60 % Allowed : 7.81 % Favored : 91.59 % 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: 1.40 (0.42), residues: 432 helix: 1.89 (0.35), residues: 229 sheet: -1.76 (0.56), residues: 75 loop : 1.14 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 305 HIS 0.005 0.001 HIS A 89 PHE 0.015 0.002 PHE A 49 TYR 0.022 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 79 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.475 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: 0.6725 (mm-40) cc_final: 0.6435 (mm-40) REVERT: A 407 GLU cc_start: 0.6776 (mp0) cc_final: 0.6435 (mp0) outliers start: 2 outliers final: 2 residues processed: 78 average time/residue: 0.2762 time to fit residues: 27.1019 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 : 0.542 ------------------------------------------------------------------------------- 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: 0.9990 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 0.0970 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.4591 r_free = 0.4591 target = 0.206683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.186636 restraints weight = 15734.791| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 3.33 r_work: 0.4259 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6090 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3339 Z= 0.284 Angle : 0.563 5.922 4529 Z= 0.301 Chirality : 0.039 0.139 525 Planarity : 0.005 0.043 580 Dihedral : 4.236 17.489 469 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.90 % Allowed : 9.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.41), residues: 432 helix: 1.55 (0.34), residues: 228 sheet: -2.06 (0.55), residues: 75 loop : 0.84 (0.56), 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 0.016 0.002 PHE A 49 TYR 0.038 0.002 TYR A 363 ARG 0.004 0.001 ARG A 329 *********************** 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 78 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6657 (mm-40) cc_final: 0.6413 (mm-40) REVERT: A 346 GLU cc_start: 0.7376 (mt-10) cc_final: 0.7091 (mt-10) outliers start: 3 outliers final: 2 residues processed: 77 average time/residue: 0.2395 time to fit residues: 23.9772 Evaluate side-chains 74 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 19 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.0870 chunk 31 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 23 optimal weight: 0.1980 overall best weight: 0.3358 ------------------------------------------------------------------------------- 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 = 0.4589 r_free = 0.4589 target = 0.205971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.185604 restraints weight = 15935.506| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 3.33 r_work: 0.4258 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 moved from start: 0.2515 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= 0.213 Angle : 0.512 7.054 4529 Z= 0.265 Chirality : 0.037 0.129 525 Planarity : 0.004 0.037 580 Dihedral : 4.073 15.967 469 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.20 % Allowed : 10.81 % 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: 0.95 (0.42), residues: 432 helix: 1.57 (0.35), residues: 228 sheet: -1.99 (0.57), residues: 74 loop : 0.88 (0.57), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 305 HIS 0.005 0.001 HIS A 290 PHE 0.011 0.001 PHE A 204 TYR 0.016 0.001 TYR A 363 ARG 0.004 0.000 ARG A 412 *********************** 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 79 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6620 (mm-40) cc_final: 0.6380 (mm-40) REVERT: A 346 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6898 (mt-10) outliers start: 4 outliers final: 3 residues processed: 76 average time/residue: 0.2234 time to fit residues: 22.4641 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 : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN 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 7 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.201077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.180726 restraints weight = 15578.213| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 3.29 r_work: 0.4177 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 3339 Z= 0.385 Angle : 0.620 7.111 4529 Z= 0.338 Chirality : 0.040 0.128 525 Planarity : 0.005 0.055 580 Dihedral : 4.710 16.208 469 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.40 % Allowed : 11.71 % 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: 0.30 (0.42), residues: 432 helix: 1.02 (0.35), residues: 225 sheet: -2.17 (0.61), residues: 66 loop : 0.34 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 305 HIS 0.010 0.002 HIS A 208 PHE 0.020 0.002 PHE A 49 TYR 0.015 0.002 TYR A 363 ARG 0.005 0.001 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 83 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6592 (mm-40) cc_final: 0.6357 (mm-40) REVERT: A 345 GLN cc_start: 0.7277 (mm110) cc_final: 0.6528 (mm110) REVERT: A 346 GLU cc_start: 0.7344 (mt-10) cc_final: 0.7014 (mt-10) outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 0.2387 time to fit residues: 24.8579 Evaluate side-chains 80 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 364 SER 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: 0.8980 chunk 1 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 chunk 10 optimal weight: 0.0870 chunk 20 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 0.3558 ------------------------------------------------------------------------------- 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 = 0.4557 r_free = 0.4557 target = 0.202043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.182490 restraints weight = 15391.894| |-----------------------------------------------------------------------------| r_work (start): 0.4343 rms_B_bonded: 3.28 r_work: 0.4231 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.3529 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 : 0.525 6.883 4529 Z= 0.276 Chirality : 0.037 0.122 525 Planarity : 0.004 0.041 580 Dihedral : 4.402 16.228 469 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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 (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: 0.39 (0.42), residues: 432 helix: 1.09 (0.35), residues: 227 sheet: -2.12 (0.61), residues: 66 loop : 0.38 (0.57), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 305 HIS 0.004 0.001 HIS A 208 PHE 0.024 0.002 PHE A 399 TYR 0.015 0.001 TYR A 363 ARG 0.003 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 75 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6535 (mm-40) cc_final: 0.6296 (mm-40) REVERT: A 151 LEU cc_start: 0.7925 (tp) cc_final: 0.7586 (tt) REVERT: A 164 GLN cc_start: 0.7835 (mt0) cc_final: 0.7590 (mt0) REVERT: A 180 ARG cc_start: 0.6604 (tpt90) cc_final: 0.5830 (tpt90) REVERT: A 345 GLN cc_start: 0.7208 (mm110) cc_final: 0.6501 (mm110) REVERT: A 346 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6710 (mt-10) outliers start: 6 outliers final: 6 residues processed: 73 average time/residue: 0.2597 time to fit residues: 24.3160 Evaluate side-chains 75 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 202 ASP Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 444 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 241 ASN ** 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 = 0.4502 r_free = 0.4502 target = 0.197262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.177681 restraints weight = 15326.815| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 3.23 r_work: 0.4171 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 3339 Z= 0.425 Angle : 0.663 7.346 4529 Z= 0.364 Chirality : 0.041 0.124 525 Planarity : 0.006 0.058 580 Dihedral : 5.098 18.215 469 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.70 % Allowed : 12.31 % 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: -0.43 (0.41), residues: 432 helix: 0.51 (0.35), residues: 225 sheet: -2.35 (0.56), residues: 75 loop : -0.04 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 305 HIS 0.007 0.002 HIS A 149 PHE 0.020 0.002 PHE A 49 TYR 0.019 0.002 TYR A 363 ARG 0.005 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 87 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.442 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 139 GLN cc_start: 0.6521 (mm-40) cc_final: 0.6315 (mm-40) REVERT: A 151 LEU cc_start: 0.8068 (tp) cc_final: 0.7824 (tt) REVERT: A 345 GLN cc_start: 0.7275 (mm110) cc_final: 0.6584 (mm110) outliers start: 9 outliers final: 7 residues processed: 82 average time/residue: 0.2524 time to fit residues: 26.4561 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 : 0.467 ------------------------------------------------------------------------------- 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 202 ASP Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 438 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4517 r_free = 0.4517 target = 0.198919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.178702 restraints weight = 15106.440| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 3.32 r_work: 0.4178 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3339 Z= 0.301 Angle : 0.582 7.009 4529 Z= 0.314 Chirality : 0.039 0.127 525 Planarity : 0.005 0.048 580 Dihedral : 4.852 17.677 469 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.80 % Allowed : 13.81 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.33 (0.41), residues: 432 helix: 0.50 (0.34), residues: 225 sheet: -2.26 (0.56), residues: 76 loop : 0.17 (0.59), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 305 HIS 0.004 0.001 HIS A 208 PHE 0.033 0.002 PHE A 399 TYR 0.019 0.002 TYR A 363 ARG 0.005 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 83 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.461 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: 0.6546 (mm-40) cc_final: 0.6337 (mm-40) REVERT: A 151 LEU cc_start: 0.8004 (tp) cc_final: 0.7802 (tt) REVERT: A 345 GLN cc_start: 0.7250 (mm110) cc_final: 0.6567 (mm110) REVERT: A 346 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6725 (mt-10) outliers start: 6 outliers final: 6 residues processed: 80 average time/residue: 0.2496 time to fit residues: 25.7539 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 : 0.483 ------------------------------------------------------------------------------- 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 185 HIS Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 285 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 6 optimal weight: 0.1980 chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 30 optimal weight: 0.0670 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 41 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 overall best weight: 0.3318 ------------------------------------------------------------------------------- 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 241 ASN ** 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 = 0.4540 r_free = 0.4540 target = 0.200631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.179805 restraints weight = 15194.244| |-----------------------------------------------------------------------------| r_work (start): 0.4318 rms_B_bonded: 3.41 r_work: 0.4197 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3339 Z= 0.226 Angle : 0.548 7.109 4529 Z= 0.290 Chirality : 0.038 0.127 525 Planarity : 0.005 0.041 580 Dihedral : 4.649 17.190 469 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.80 % Allowed : 14.11 % Favored : 84.08 % 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: -0.11 (0.42), residues: 432 helix: 0.63 (0.34), residues: 225 sheet: -2.14 (0.56), residues: 76 loop : 0.38 (0.60), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 305 HIS 0.004 0.001 HIS A 185 PHE 0.031 0.002 PHE A 399 TYR 0.020 0.002 TYR A 363 ARG 0.004 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 83 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.6621 (tpt90) cc_final: 0.5973 (tpt90) REVERT: A 345 GLN cc_start: 0.7224 (mm110) cc_final: 0.6546 (mm110) REVERT: A 346 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6757 (mt-10) outliers start: 6 outliers final: 6 residues processed: 81 average time/residue: 0.2535 time to fit residues: 26.6287 Evaluate side-chains 81 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 202 ASP Chi-restraints excluded: chain A residue 285 ASN 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 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 41 optimal weight: 0.0470 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 17 optimal weight: 0.0870 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 overall best weight: 0.3656 ------------------------------------------------------------------------------- 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 = 0.4541 r_free = 0.4541 target = 0.200470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.179736 restraints weight = 15443.340| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 3.45 r_work: 0.4194 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3339 Z= 0.234 Angle : 0.566 7.286 4529 Z= 0.296 Chirality : 0.038 0.129 525 Planarity : 0.004 0.036 580 Dihedral : 4.602 16.764 469 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.10 % Allowed : 15.32 % Favored : 82.58 % 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: -0.03 (0.42), residues: 432 helix: 0.64 (0.34), residues: 225 sheet: -2.07 (0.56), residues: 76 loop : 0.49 (0.62), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 305 HIS 0.004 0.001 HIS A 185 PHE 0.030 0.002 PHE A 399 TYR 0.015 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 82 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.6618 (tpt90) cc_final: 0.6014 (tpt90) REVERT: A 345 GLN cc_start: 0.7192 (mm110) cc_final: 0.6511 (mm110) REVERT: A 346 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6755 (mt-10) outliers start: 7 outliers final: 7 residues processed: 79 average time/residue: 0.2610 time to fit residues: 26.5316 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 : 0.496 ------------------------------------------------------------------------------- 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 185 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 37 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 4 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.0770 overall best weight: 0.3138 ------------------------------------------------------------------------------- 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 = 0.4543 r_free = 0.4543 target = 0.200520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.179663 restraints weight = 15712.179| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 3.50 r_work: 0.4198 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 0.4718 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= 0.217 Angle : 0.555 7.849 4529 Z= 0.290 Chirality : 0.038 0.129 525 Planarity : 0.004 0.035 580 Dihedral : 4.545 16.095 469 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.80 % Allowed : 15.92 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.42), residues: 432 helix: 0.65 (0.34), residues: 225 sheet: -1.98 (0.56), residues: 76 loop : 0.44 (0.60), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 305 HIS 0.008 0.001 HIS A 185 PHE 0.026 0.002 PHE A 399 TYR 0.015 0.002 TYR A 363 ARG 0.004 0.000 ARG A 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4991.80 seconds wall clock time: 88 minutes 16.49 seconds (5296.49 seconds total)