Starting phenix.real_space_refine on Sun Apr 27 06:28:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kdt_37145/04_2025/8kdt_37145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kdt_37145/04_2025/8kdt_37145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kdt_37145/04_2025/8kdt_37145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kdt_37145/04_2025/8kdt_37145.map" model { file = "/net/cci-nas-00/data/ceres_data/8kdt_37145/04_2025/8kdt_37145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kdt_37145/04_2025/8kdt_37145.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 3075 2.51 5 N 803 2.21 5 O 937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4837 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1546 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 14, 'TRANS': 179} Chain: "H" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "L" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1653 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 12, 'TRANS': 200} Time building chain proxies: 4.19, per 1000 atoms: 0.87 Number of scatterers: 4837 At special positions: 0 Unit cell: (72.696, 106.248, 103.452, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 937 8.00 N 803 7.00 C 3075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " 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: 1.13 Conformation dependent library (CDL) restraints added in 644.0 milliseconds 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 11 sheets defined 5.3% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.743A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 removed outlier: 3.698A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 138 removed outlier: 3.843A pdb=" N THR H 138 " --> pdb=" O SER H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 196 Processing helix chain 'L' and resid 123 through 128 removed outlier: 3.613A pdb=" N LEU L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS L 128 " --> pdb=" O ASP L 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 123 through 128' Processing helix chain 'L' and resid 184 through 189 removed outlier: 3.806A pdb=" N GLU L 189 " --> pdb=" O LYS L 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 341 through 342 removed outlier: 3.691A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 498 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 494 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 422 " --> pdb=" O THR A 363 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.590A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.825A pdb=" N THR H 119 " --> pdb=" O GLU H 10 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 50 through 51 Processing sheet with id=AA6, first strand: chain 'H' and resid 172 through 177 removed outlier: 5.281A pdb=" N SER H 186 " --> pdb=" O PRO H 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.621A pdb=" N TYR L 86 " --> pdb=" O THR L 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 21 through 23 removed outlier: 3.665A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.462A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 116 through 120 removed outlier: 3.600A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 146 through 152 removed outlier: 3.956A pdb=" N ALA L 195 " --> pdb=" O LYS L 151 " (cutoff:3.500A) 98 hydrogen bonds defined for protein. 240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1525 1.34 - 1.46: 1238 1.46 - 1.58: 2174 1.58 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 4965 Sorted by residual: bond pdb=" C PRO A 469 " pdb=" N PRO A 470 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.25e+00 bond pdb=" C TRP L 94 " pdb=" N PRO L 95 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.50e-01 bond pdb=" CA VAL L 152 " pdb=" CB VAL L 152 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.31e-02 5.83e+03 8.88e-01 bond pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.70e-01 bond pdb=" CA TRP H 47 " pdb=" CB TRP H 47 " ideal model delta sigma weight residual 1.532 1.549 -0.016 2.01e-02 2.48e+03 6.57e-01 ... (remaining 4960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 6540 1.21 - 2.42: 172 2.42 - 3.63: 41 3.63 - 4.84: 7 4.84 - 6.05: 6 Bond angle restraints: 6766 Sorted by residual: angle pdb=" CA TRP H 47 " pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 113.60 119.10 -5.50 1.90e+00 2.77e-01 8.38e+00 angle pdb=" N VAL H 120 " pdb=" CA VAL H 120 " pdb=" C VAL H 120 " ideal model delta sigma weight residual 106.61 110.59 -3.98 1.78e+00 3.16e-01 5.00e+00 angle pdb=" C ASP H 54 " pdb=" N ALA H 55 " pdb=" CA ALA H 55 " ideal model delta sigma weight residual 122.17 118.73 3.44 1.54e+00 4.22e-01 4.98e+00 angle pdb=" N GLU H 155 " pdb=" CA GLU H 155 " pdb=" C GLU H 155 " ideal model delta sigma weight residual 109.81 114.49 -4.68 2.21e+00 2.05e-01 4.49e+00 angle pdb=" C LEU A 448 " pdb=" N ARG A 449 " pdb=" CA ARG A 449 " ideal model delta sigma weight residual 122.71 128.72 -6.01 3.03e+00 1.09e-01 3.94e+00 ... (remaining 6761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.32: 2697 10.32 - 20.63: 168 20.63 - 30.95: 69 30.95 - 41.26: 16 41.26 - 51.58: 8 Dihedral angle restraints: 2958 sinusoidal: 1134 harmonic: 1824 Sorted by residual: dihedral pdb=" CA GLU H 46 " pdb=" C GLU H 46 " pdb=" N TRP H 47 " pdb=" CA TRP H 47 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA GLU H 155 " pdb=" C GLU H 155 " pdb=" N PRO H 156 " pdb=" CA PRO H 156 " ideal model delta harmonic sigma weight residual 180.00 157.23 22.77 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ARG H 38 " pdb=" CB ARG H 38 " pdb=" CG ARG H 38 " pdb=" CD ARG H 38 " ideal model delta sinusoidal sigma weight residual -60.00 -111.58 51.58 3 1.50e+01 4.44e-03 9.03e+00 ... (remaining 2955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 426 0.025 - 0.050: 192 0.050 - 0.076: 68 0.076 - 0.101: 46 0.101 - 0.126: 18 Chirality restraints: 750 Sorted by residual: chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA ILE L 58 " pdb=" N ILE L 58 " pdb=" C ILE L 58 " pdb=" CB ILE L 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE A 397 " pdb=" N ILE A 397 " pdb=" C ILE A 397 " pdb=" CB ILE A 397 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.24e-01 ... (remaining 747 not shown) Planarity restraints: 867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 14 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO L 15 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO H 14 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " 0.011 2.00e-02 2.50e+03 8.65e-03 1.87e+00 pdb=" CG TRP H 47 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " 0.002 2.00e-02 2.50e+03 ... (remaining 864 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 814 2.77 - 3.30: 4271 3.30 - 3.84: 7761 3.84 - 4.37: 8839 4.37 - 4.90: 15418 Nonbonded interactions: 37103 Sorted by model distance: nonbonded pdb=" OG SER A 380 " pdb=" O GLU A 502 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR A 436 " pdb=" OH TYR A 484 " model vdw 2.285 3.040 nonbonded pdb=" OD1 ASP L 172 " pdb=" OG1 THR L 174 " model vdw 2.291 3.040 nonbonded pdb=" O ALA H 106 " pdb=" NH1 ARG L 91 " model vdw 2.294 3.120 nonbonded pdb=" OD2 ASP A 429 " pdb=" OH TYR A 438 " model vdw 2.299 3.040 ... (remaining 37098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 16.630 Find NCS groups from input model: 0.080 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 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 0.026 4973 Z= 0.100 Angle : 0.514 6.049 6782 Z= 0.283 Chirality : 0.039 0.126 750 Planarity : 0.004 0.037 867 Dihedral : 8.532 51.579 1768 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 5.91 % Allowed : 5.73 % Favored : 88.35 % 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: -4.43 (0.29), residues: 619 helix: -5.41 (0.31), residues: 6 sheet: -2.84 (0.30), residues: 217 loop : -3.10 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 47 HIS 0.001 0.000 HIS L 90 PHE 0.009 0.001 PHE A 360 TYR 0.006 0.001 TYR L 49 ARG 0.001 0.000 ARG L 54 Details of bonding type rmsd hydrogen bonds : bond 0.30134 ( 98) hydrogen bonds : angle 10.56742 ( 240) SS BOND : bond 0.00130 ( 8) SS BOND : angle 0.42018 ( 16) covalent geometry : bond 0.00192 ( 4965) covalent geometry : angle 0.51451 ( 6766) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 447 LYS cc_start: 0.7994 (mttm) cc_final: 0.7772 (mttm) REVERT: A 473 ASN cc_start: 0.7536 (m-40) cc_final: 0.7310 (m-40) REVERT: A 510 VAL cc_start: 0.7269 (OUTLIER) cc_final: 0.6959 (m) REVERT: H 57 SER cc_start: 0.7623 (m) cc_final: 0.7358 (t) REVERT: H 78 THR cc_start: 0.8431 (m) cc_final: 0.7930 (p) REVERT: H 145 LEU cc_start: 0.8025 (mt) cc_final: 0.7631 (mt) REVERT: H 187 SER cc_start: 0.7639 (t) cc_final: 0.7385 (m) REVERT: H 216 LYS cc_start: 0.8452 (tppt) cc_final: 0.8204 (tppp) REVERT: L 18 ARG cc_start: 0.7356 (ptm-80) cc_final: 0.7110 (ptm-80) outliers start: 32 outliers final: 14 residues processed: 194 average time/residue: 0.1231 time to fit residues: 32.1048 Evaluate side-chains 174 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 32 HIS Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 171 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN A 473 ASN H 32 HIS H 178 GLN L 37 GLN L 89 GLN L 102 GLN ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.146350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.130125 restraints weight = 7414.903| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.90 r_work: 0.3707 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4973 Z= 0.178 Angle : 0.643 6.652 6782 Z= 0.326 Chirality : 0.046 0.228 750 Planarity : 0.005 0.040 867 Dihedral : 6.435 48.559 708 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 6.28 % Allowed : 13.86 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.65 (0.32), residues: 619 helix: -5.39 (0.31), residues: 6 sheet: -1.99 (0.34), residues: 225 loop : -2.76 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 47 HIS 0.005 0.001 HIS L 90 PHE 0.016 0.002 PHE A 360 TYR 0.024 0.002 TYR A 442 ARG 0.002 0.000 ARG L 144 Details of bonding type rmsd hydrogen bonds : bond 0.04447 ( 98) hydrogen bonds : angle 6.50353 ( 240) SS BOND : bond 0.00467 ( 8) SS BOND : angle 1.98423 ( 16) covalent geometry : bond 0.00390 ( 4965) covalent geometry : angle 0.63655 ( 6766) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7395 (m-40) cc_final: 0.7137 (m-40) REVERT: A 342 ARG cc_start: 0.8007 (ptp-110) cc_final: 0.7775 (ptp-110) REVERT: A 360 PHE cc_start: 0.6372 (OUTLIER) cc_final: 0.5762 (p90) REVERT: A 447 LYS cc_start: 0.8242 (mttm) cc_final: 0.7961 (mttm) REVERT: H 36 TRP cc_start: 0.7866 (m100) cc_final: 0.7579 (m100) REVERT: H 69 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8130 (p) REVERT: H 71 THR cc_start: 0.8423 (t) cc_final: 0.8123 (p) REVERT: H 114 GLN cc_start: 0.8357 (pt0) cc_final: 0.8132 (pm20) REVERT: H 145 LEU cc_start: 0.8375 (mt) cc_final: 0.8045 (mt) REVERT: H 187 SER cc_start: 0.8199 (t) cc_final: 0.7904 (m) REVERT: H 216 LYS cc_start: 0.8707 (tppt) cc_final: 0.8434 (tppp) REVERT: H 217 LYS cc_start: 0.8656 (tttt) cc_final: 0.8369 (tttt) REVERT: L 18 ARG cc_start: 0.7819 (ptm-80) cc_final: 0.7515 (ptm-80) REVERT: L 22 SER cc_start: 0.8383 (p) cc_final: 0.8015 (m) REVERT: L 46 LEU cc_start: 0.7779 (tp) cc_final: 0.7532 (tp) REVERT: L 138 LEU cc_start: 0.7435 (mm) cc_final: 0.7229 (mp) REVERT: L 157 GLN cc_start: 0.7449 (tp40) cc_final: 0.7127 (tp40) REVERT: L 164 SER cc_start: 0.8530 (t) cc_final: 0.7913 (p) REVERT: L 172 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7218 (p0) outliers start: 34 outliers final: 19 residues processed: 187 average time/residue: 0.1593 time to fit residues: 39.8029 Evaluate side-chains 179 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 110 ARG Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 184 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 44 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 14 optimal weight: 0.0170 chunk 35 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN H 178 GLN L 27 GLN L 38 GLN L 160 ASN ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.145126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.129729 restraints weight = 7468.016| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.73 r_work: 0.3720 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4973 Z= 0.145 Angle : 0.615 8.597 6782 Z= 0.308 Chirality : 0.045 0.261 750 Planarity : 0.005 0.040 867 Dihedral : 6.185 48.996 701 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 5.73 % Allowed : 18.85 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.24 (0.33), residues: 619 helix: -5.38 (0.31), residues: 6 sheet: -1.79 (0.34), residues: 228 loop : -2.42 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 PHE 0.018 0.002 PHE A 416 TYR 0.029 0.002 TYR A 442 ARG 0.002 0.000 ARG L 91 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 98) hydrogen bonds : angle 5.89669 ( 240) SS BOND : bond 0.00950 ( 8) SS BOND : angle 1.68770 ( 16) covalent geometry : bond 0.00328 ( 4965) covalent geometry : angle 0.60988 ( 6766) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7421 (m-40) cc_final: 0.7167 (m-40) REVERT: A 342 ARG cc_start: 0.7986 (ptp-110) cc_final: 0.7687 (ptp-170) REVERT: A 447 LYS cc_start: 0.8166 (mttm) cc_final: 0.7913 (mttm) REVERT: H 36 TRP cc_start: 0.7853 (m100) cc_final: 0.7574 (m100) REVERT: H 69 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8181 (p) REVERT: H 71 THR cc_start: 0.8375 (t) cc_final: 0.8092 (p) REVERT: H 91 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7955 (p) REVERT: H 145 LEU cc_start: 0.8403 (mt) cc_final: 0.8056 (mt) REVERT: H 187 SER cc_start: 0.8187 (t) cc_final: 0.7939 (m) REVERT: H 216 LYS cc_start: 0.8634 (tppt) cc_final: 0.8428 (tppp) REVERT: H 217 LYS cc_start: 0.8579 (tttt) cc_final: 0.8319 (tttt) REVERT: L 18 ARG cc_start: 0.7729 (ptm-80) cc_final: 0.7473 (ptm-80) REVERT: L 22 SER cc_start: 0.8365 (p) cc_final: 0.8047 (m) REVERT: L 160 ASN cc_start: 0.7004 (m110) cc_final: 0.6779 (m110) REVERT: L 164 SER cc_start: 0.8518 (t) cc_final: 0.8019 (p) REVERT: L 172 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7112 (p0) REVERT: L 175 TYR cc_start: 0.7924 (m-80) cc_final: 0.7274 (m-80) outliers start: 31 outliers final: 22 residues processed: 177 average time/residue: 0.1448 time to fit residues: 34.3692 Evaluate side-chains 182 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 110 ARG Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 184 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 49 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 191 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 = 0.3957 r_free = 0.3957 target = 0.139892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.124013 restraints weight = 7547.645| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.84 r_work: 0.3626 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 4973 Z= 0.258 Angle : 0.696 8.638 6782 Z= 0.356 Chirality : 0.048 0.301 750 Planarity : 0.005 0.042 867 Dihedral : 6.776 50.572 701 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 5.91 % Allowed : 19.59 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.10 (0.33), residues: 619 helix: -5.38 (0.30), residues: 6 sheet: -1.62 (0.34), residues: 223 loop : -2.36 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 47 HIS 0.004 0.001 HIS L 90 PHE 0.023 0.002 PHE A 501 TYR 0.032 0.002 TYR A 442 ARG 0.003 0.001 ARG L 91 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 98) hydrogen bonds : angle 5.66417 ( 240) SS BOND : bond 0.00812 ( 8) SS BOND : angle 1.82647 ( 16) covalent geometry : bond 0.00568 ( 4965) covalent geometry : angle 0.69079 ( 6766) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7410 (m-40) cc_final: 0.7187 (m-40) REVERT: A 342 ARG cc_start: 0.8066 (ptp-110) cc_final: 0.7259 (ptp-110) REVERT: A 436 TYR cc_start: 0.8230 (m-80) cc_final: 0.7982 (m-80) REVERT: A 447 LYS cc_start: 0.8331 (mttm) cc_final: 0.8093 (mttm) REVERT: A 451 PHE cc_start: 0.7873 (m-10) cc_final: 0.7612 (m-10) REVERT: A 457 ASN cc_start: 0.8368 (t0) cc_final: 0.7977 (t0) REVERT: H 36 TRP cc_start: 0.7872 (m100) cc_final: 0.7548 (m100) REVERT: H 69 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8198 (p) REVERT: H 71 THR cc_start: 0.8396 (t) cc_final: 0.8143 (p) REVERT: H 90 ASP cc_start: 0.8391 (m-30) cc_final: 0.8108 (t0) REVERT: H 152 TYR cc_start: 0.7312 (p90) cc_final: 0.6646 (p90) REVERT: H 185 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8300 (tp) REVERT: H 188 VAL cc_start: 0.8616 (t) cc_final: 0.8360 (p) REVERT: H 216 LYS cc_start: 0.8783 (tppt) cc_final: 0.8530 (tppp) REVERT: H 217 LYS cc_start: 0.8692 (tttt) cc_final: 0.8416 (tttt) REVERT: L 18 ARG cc_start: 0.7813 (ptm-80) cc_final: 0.7491 (ptm-80) REVERT: L 22 SER cc_start: 0.8429 (p) cc_final: 0.8111 (m) REVERT: L 24 ARG cc_start: 0.7293 (ttm110) cc_final: 0.6930 (ptp-110) REVERT: L 89 GLN cc_start: 0.8092 (tt0) cc_final: 0.7847 (tt0) REVERT: L 164 SER cc_start: 0.8529 (t) cc_final: 0.7978 (p) REVERT: L 172 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7076 (p0) REVERT: L 173 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.8230 (p) REVERT: L 175 TYR cc_start: 0.8167 (m-80) cc_final: 0.7647 (m-80) REVERT: L 201 GLN cc_start: 0.8335 (tt0) cc_final: 0.8129 (tt0) outliers start: 32 outliers final: 23 residues processed: 180 average time/residue: 0.1669 time to fit residues: 40.5636 Evaluate side-chains 185 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 110 ARG Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 173 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 0.0170 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 0.0980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN L 191 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.142721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.126646 restraints weight = 7532.565| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.89 r_work: 0.3673 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 4973 Z= 0.130 Angle : 0.636 9.879 6782 Z= 0.315 Chirality : 0.045 0.260 750 Planarity : 0.005 0.042 867 Dihedral : 6.381 49.799 699 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 5.91 % Allowed : 21.81 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.93 (0.33), residues: 619 helix: -5.38 (0.30), residues: 6 sheet: -1.38 (0.33), residues: 223 loop : -2.33 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.025 0.002 PHE A 501 TYR 0.030 0.002 TYR A 442 ARG 0.003 0.000 ARG L 91 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 98) hydrogen bonds : angle 5.58066 ( 240) SS BOND : bond 0.00631 ( 8) SS BOND : angle 1.90720 ( 16) covalent geometry : bond 0.00303 ( 4965) covalent geometry : angle 0.62970 ( 6766) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 379 PHE cc_start: 0.6706 (m-10) cc_final: 0.6309 (m-10) REVERT: A 436 TYR cc_start: 0.8171 (m-80) cc_final: 0.7960 (m-80) REVERT: A 447 LYS cc_start: 0.8207 (mttm) cc_final: 0.7933 (mttm) REVERT: A 451 PHE cc_start: 0.7723 (m-10) cc_final: 0.7505 (m-10) REVERT: A 457 ASN cc_start: 0.8363 (t0) cc_final: 0.7975 (t0) REVERT: H 36 TRP cc_start: 0.7889 (m100) cc_final: 0.7520 (m100) REVERT: H 69 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8179 (p) REVERT: H 71 THR cc_start: 0.8335 (t) cc_final: 0.8073 (p) REVERT: H 90 ASP cc_start: 0.8357 (m-30) cc_final: 0.8076 (t0) REVERT: H 91 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.8061 (p) REVERT: H 114 GLN cc_start: 0.8306 (pm20) cc_final: 0.8079 (pm20) REVERT: H 145 LEU cc_start: 0.8499 (mt) cc_final: 0.8223 (mt) REVERT: H 187 SER cc_start: 0.8131 (t) cc_final: 0.7910 (m) REVERT: H 188 VAL cc_start: 0.8572 (t) cc_final: 0.8329 (p) REVERT: H 216 LYS cc_start: 0.8739 (tppt) cc_final: 0.8463 (tppp) REVERT: H 217 LYS cc_start: 0.8693 (tttt) cc_final: 0.8417 (tttt) REVERT: L 18 ARG cc_start: 0.7835 (ptm-80) cc_final: 0.7545 (ptm-80) REVERT: L 22 SER cc_start: 0.8394 (p) cc_final: 0.8044 (m) REVERT: L 164 SER cc_start: 0.8546 (t) cc_final: 0.8064 (p) REVERT: L 172 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7004 (p0) REVERT: L 173 SER cc_start: 0.8726 (OUTLIER) cc_final: 0.8192 (p) REVERT: L 175 TYR cc_start: 0.8132 (m-80) cc_final: 0.7666 (m-80) outliers start: 32 outliers final: 22 residues processed: 168 average time/residue: 0.1249 time to fit residues: 28.5783 Evaluate side-chains 172 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 338 TYR Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 110 ARG Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 173 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.138938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.123100 restraints weight = 7512.853| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.87 r_work: 0.3620 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 4973 Z= 0.233 Angle : 0.704 10.541 6782 Z= 0.352 Chirality : 0.047 0.275 750 Planarity : 0.005 0.040 867 Dihedral : 6.811 51.637 699 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 6.84 % Allowed : 21.26 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.84 (0.33), residues: 619 helix: -5.37 (0.30), residues: 6 sheet: -1.38 (0.34), residues: 222 loop : -2.23 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 47 HIS 0.005 0.002 HIS L 191 PHE 0.024 0.002 PHE A 360 TYR 0.033 0.002 TYR A 442 ARG 0.003 0.001 ARG L 91 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 98) hydrogen bonds : angle 5.66262 ( 240) SS BOND : bond 0.00407 ( 8) SS BOND : angle 1.96945 ( 16) covalent geometry : bond 0.00519 ( 4965) covalent geometry : angle 0.69819 ( 6766) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7401 (m-40) cc_final: 0.7189 (m-40) REVERT: A 334 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7151 (m-10) REVERT: A 342 ARG cc_start: 0.8062 (ptp-110) cc_final: 0.7210 (ptp-110) REVERT: A 364 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7621 (t80) REVERT: A 436 TYR cc_start: 0.8249 (m-80) cc_final: 0.7863 (m-80) REVERT: A 447 LYS cc_start: 0.8338 (mttm) cc_final: 0.8075 (mttm) REVERT: A 451 PHE cc_start: 0.7796 (m-10) cc_final: 0.7555 (m-10) REVERT: H 36 TRP cc_start: 0.7893 (m100) cc_final: 0.7556 (m100) REVERT: H 69 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8190 (p) REVERT: H 71 THR cc_start: 0.8361 (t) cc_final: 0.8110 (p) REVERT: H 90 ASP cc_start: 0.8410 (m-30) cc_final: 0.8122 (t0) REVERT: H 114 GLN cc_start: 0.8415 (pm20) cc_final: 0.8097 (pm20) REVERT: H 145 LEU cc_start: 0.8497 (mt) cc_final: 0.8228 (mt) REVERT: H 188 VAL cc_start: 0.8612 (t) cc_final: 0.8362 (p) REVERT: H 216 LYS cc_start: 0.8765 (tppt) cc_final: 0.8497 (tppp) REVERT: H 217 LYS cc_start: 0.8742 (tttt) cc_final: 0.8473 (tttt) REVERT: L 18 ARG cc_start: 0.7837 (ptm-80) cc_final: 0.7564 (ptm-80) REVERT: L 22 SER cc_start: 0.8442 (p) cc_final: 0.8119 (m) REVERT: L 24 ARG cc_start: 0.7494 (ttm110) cc_final: 0.7017 (ptp-110) REVERT: L 89 GLN cc_start: 0.8117 (tt0) cc_final: 0.7822 (tt0) REVERT: L 164 SER cc_start: 0.8514 (t) cc_final: 0.8029 (p) REVERT: L 172 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7042 (p0) REVERT: L 173 SER cc_start: 0.8831 (OUTLIER) cc_final: 0.8294 (p) REVERT: L 175 TYR cc_start: 0.8188 (m-80) cc_final: 0.7811 (m-80) REVERT: L 201 GLN cc_start: 0.8356 (tt0) cc_final: 0.8108 (tt0) outliers start: 37 outliers final: 27 residues processed: 178 average time/residue: 0.1315 time to fit residues: 31.4650 Evaluate side-chains 185 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 338 TYR Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 110 ARG Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 173 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.0070 chunk 34 optimal weight: 0.3980 chunk 49 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 52 optimal weight: 0.0070 overall best weight: 0.1816 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.143095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.127842 restraints weight = 7332.947| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.71 r_work: 0.3697 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 4973 Z= 0.114 Angle : 0.639 11.231 6782 Z= 0.314 Chirality : 0.044 0.262 750 Planarity : 0.005 0.042 867 Dihedral : 6.450 50.589 699 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 5.55 % Allowed : 22.74 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.67 (0.33), residues: 619 helix: -5.38 (0.30), residues: 6 sheet: -1.24 (0.33), residues: 228 loop : -2.13 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 47 HIS 0.004 0.001 HIS L 191 PHE 0.013 0.002 PHE A 379 TYR 0.029 0.001 TYR A 442 ARG 0.002 0.000 ARG L 91 Details of bonding type rmsd hydrogen bonds : bond 0.02783 ( 98) hydrogen bonds : angle 5.31047 ( 240) SS BOND : bond 0.00815 ( 8) SS BOND : angle 2.05199 ( 16) covalent geometry : bond 0.00272 ( 4965) covalent geometry : angle 0.63181 ( 6766) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.842 Fit side-chains REVERT: A 330 ASN cc_start: 0.7353 (m-40) cc_final: 0.7148 (m-40) REVERT: A 436 TYR cc_start: 0.8137 (m-80) cc_final: 0.7834 (m-80) REVERT: A 447 LYS cc_start: 0.8156 (mttm) cc_final: 0.7917 (mttm) REVERT: A 457 ASN cc_start: 0.8370 (t0) cc_final: 0.8089 (t0) REVERT: H 36 TRP cc_start: 0.7847 (m100) cc_final: 0.7565 (m100) REVERT: H 69 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8229 (p) REVERT: H 71 THR cc_start: 0.8340 (t) cc_final: 0.8104 (p) REVERT: H 90 ASP cc_start: 0.8227 (m-30) cc_final: 0.7998 (t0) REVERT: H 91 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.8029 (p) REVERT: H 114 GLN cc_start: 0.8238 (pm20) cc_final: 0.7966 (pm20) REVERT: H 145 LEU cc_start: 0.8496 (mt) cc_final: 0.8215 (mt) REVERT: H 216 LYS cc_start: 0.8702 (tppt) cc_final: 0.8460 (tppp) REVERT: H 217 LYS cc_start: 0.8652 (tttt) cc_final: 0.8413 (tttt) REVERT: L 18 ARG cc_start: 0.7792 (ptm-80) cc_final: 0.7562 (ptm-80) REVERT: L 22 SER cc_start: 0.8372 (p) cc_final: 0.8041 (m) REVERT: L 89 GLN cc_start: 0.8081 (tt0) cc_final: 0.7826 (tt0) REVERT: L 97 MET cc_start: 0.6812 (ttm) cc_final: 0.6384 (ttm) REVERT: L 164 SER cc_start: 0.8439 (t) cc_final: 0.7937 (p) REVERT: L 173 SER cc_start: 0.8757 (OUTLIER) cc_final: 0.8289 (p) REVERT: L 175 TYR cc_start: 0.8141 (m-80) cc_final: 0.7736 (m-80) REVERT: L 201 GLN cc_start: 0.8192 (tt0) cc_final: 0.7982 (tt0) outliers start: 30 outliers final: 24 residues processed: 165 average time/residue: 0.1396 time to fit residues: 32.2929 Evaluate side-chains 173 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 338 TYR Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 173 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 0.0060 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.141202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.125507 restraints weight = 7442.098| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.83 r_work: 0.3651 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 4973 Z= 0.160 Angle : 0.655 12.109 6782 Z= 0.325 Chirality : 0.045 0.279 750 Planarity : 0.005 0.040 867 Dihedral : 6.602 51.901 699 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 7.21 % Allowed : 22.00 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.56 (0.33), residues: 619 helix: -4.76 (0.48), residues: 12 sheet: -0.96 (0.35), residues: 220 loop : -2.13 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 47 HIS 0.005 0.001 HIS L 191 PHE 0.016 0.002 PHE A 360 TYR 0.033 0.002 TYR A 442 ARG 0.002 0.000 ARG L 91 Details of bonding type rmsd hydrogen bonds : bond 0.03109 ( 98) hydrogen bonds : angle 5.23255 ( 240) SS BOND : bond 0.00764 ( 8) SS BOND : angle 1.98407 ( 16) covalent geometry : bond 0.00366 ( 4965) covalent geometry : angle 0.64848 ( 6766) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.527 Fit side-chains REVERT: A 330 ASN cc_start: 0.7381 (m-40) cc_final: 0.7169 (m-40) REVERT: A 334 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.7134 (m-10) REVERT: A 436 TYR cc_start: 0.8220 (m-80) cc_final: 0.7884 (m-80) REVERT: A 447 LYS cc_start: 0.8281 (mttm) cc_final: 0.7984 (mttm) REVERT: A 451 PHE cc_start: 0.7727 (m-10) cc_final: 0.7524 (m-10) REVERT: A 457 ASN cc_start: 0.8396 (t0) cc_final: 0.8036 (t0) REVERT: H 36 TRP cc_start: 0.7868 (m100) cc_final: 0.7542 (m100) REVERT: H 69 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8218 (p) REVERT: H 71 THR cc_start: 0.8332 (t) cc_final: 0.8085 (p) REVERT: H 90 ASP cc_start: 0.8369 (m-30) cc_final: 0.8083 (t0) REVERT: H 91 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8146 (p) REVERT: H 114 GLN cc_start: 0.8336 (pm20) cc_final: 0.8044 (pm20) REVERT: H 145 LEU cc_start: 0.8477 (mt) cc_final: 0.8170 (mt) REVERT: H 216 LYS cc_start: 0.8734 (tppt) cc_final: 0.8468 (tppp) REVERT: H 217 LYS cc_start: 0.8739 (tttt) cc_final: 0.8485 (tttt) REVERT: L 18 ARG cc_start: 0.7832 (ptm-80) cc_final: 0.7576 (ptm-80) REVERT: L 22 SER cc_start: 0.8403 (p) cc_final: 0.8075 (m) REVERT: L 24 ARG cc_start: 0.7505 (ttm110) cc_final: 0.6970 (ptp-110) REVERT: L 89 GLN cc_start: 0.8146 (tt0) cc_final: 0.7732 (tt0) REVERT: L 164 SER cc_start: 0.8482 (t) cc_final: 0.7934 (p) REVERT: L 172 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.7031 (p0) REVERT: L 173 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8304 (p) REVERT: L 175 TYR cc_start: 0.8187 (m-80) cc_final: 0.7801 (m-80) REVERT: L 201 GLN cc_start: 0.8276 (tt0) cc_final: 0.7964 (tt0) outliers start: 39 outliers final: 29 residues processed: 176 average time/residue: 0.1467 time to fit residues: 35.4567 Evaluate side-chains 186 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 338 TYR Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 194 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 49 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.0670 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.140961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.125365 restraints weight = 7395.215| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.80 r_work: 0.3653 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 4973 Z= 0.158 Angle : 0.668 12.374 6782 Z= 0.330 Chirality : 0.045 0.278 750 Planarity : 0.005 0.041 867 Dihedral : 6.697 52.354 699 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 6.65 % Allowed : 22.74 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.41 (0.34), residues: 619 helix: -4.72 (0.50), residues: 12 sheet: -0.86 (0.35), residues: 220 loop : -2.03 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 47 HIS 0.005 0.001 HIS L 191 PHE 0.016 0.002 PHE L 62 TYR 0.032 0.002 TYR A 442 ARG 0.002 0.000 ARG L 91 Details of bonding type rmsd hydrogen bonds : bond 0.03152 ( 98) hydrogen bonds : angle 5.20738 ( 240) SS BOND : bond 0.00741 ( 8) SS BOND : angle 1.96828 ( 16) covalent geometry : bond 0.00365 ( 4965) covalent geometry : angle 0.66184 ( 6766) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7397 (m-40) cc_final: 0.7182 (m-40) REVERT: A 334 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7144 (m-10) REVERT: A 436 TYR cc_start: 0.8219 (m-80) cc_final: 0.7839 (m-80) REVERT: A 447 LYS cc_start: 0.8267 (mttm) cc_final: 0.7953 (mttm) REVERT: A 457 ASN cc_start: 0.8387 (t0) cc_final: 0.7969 (t0) REVERT: H 36 TRP cc_start: 0.7850 (m100) cc_final: 0.7533 (m100) REVERT: H 69 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.8231 (p) REVERT: H 71 THR cc_start: 0.8326 (t) cc_final: 0.8085 (p) REVERT: H 90 ASP cc_start: 0.8359 (m-30) cc_final: 0.8110 (t0) REVERT: H 91 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8164 (p) REVERT: H 114 GLN cc_start: 0.8345 (pm20) cc_final: 0.8065 (pm20) REVERT: H 145 LEU cc_start: 0.8516 (mt) cc_final: 0.8195 (mt) REVERT: H 216 LYS cc_start: 0.8711 (tppt) cc_final: 0.8446 (tppp) REVERT: H 217 LYS cc_start: 0.8743 (tttt) cc_final: 0.8491 (tttt) REVERT: L 18 ARG cc_start: 0.7845 (ptm-80) cc_final: 0.7583 (ptm-80) REVERT: L 22 SER cc_start: 0.8395 (p) cc_final: 0.8083 (m) REVERT: L 24 ARG cc_start: 0.7516 (ttm110) cc_final: 0.6991 (ptp-110) REVERT: L 89 GLN cc_start: 0.8170 (tt0) cc_final: 0.7853 (tt0) REVERT: L 172 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.7011 (p0) REVERT: L 173 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8312 (p) REVERT: L 175 TYR cc_start: 0.8203 (m-80) cc_final: 0.7829 (m-80) REVERT: L 201 GLN cc_start: 0.8296 (tt0) cc_final: 0.7975 (tt0) outliers start: 36 outliers final: 29 residues processed: 175 average time/residue: 0.1501 time to fit residues: 35.8395 Evaluate side-chains 186 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 338 TYR Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 110 ARG Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 194 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 52 optimal weight: 0.0060 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 59 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.141523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.125846 restraints weight = 7499.959| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.82 r_work: 0.3658 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 4973 Z= 0.142 Angle : 0.669 12.204 6782 Z= 0.330 Chirality : 0.045 0.262 750 Planarity : 0.005 0.043 867 Dihedral : 6.736 52.398 699 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 6.47 % Allowed : 23.29 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.28 (0.34), residues: 619 helix: -4.62 (0.59), residues: 12 sheet: -0.74 (0.36), residues: 220 loop : -1.97 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 47 HIS 0.005 0.001 HIS L 191 PHE 0.025 0.002 PHE A 451 TYR 0.032 0.002 TYR A 442 ARG 0.002 0.000 ARG L 91 Details of bonding type rmsd hydrogen bonds : bond 0.03089 ( 98) hydrogen bonds : angle 5.16965 ( 240) SS BOND : bond 0.00729 ( 8) SS BOND : angle 1.88453 ( 16) covalent geometry : bond 0.00332 ( 4965) covalent geometry : angle 0.66305 ( 6766) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7408 (m-40) cc_final: 0.7198 (m-40) REVERT: A 334 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.7093 (m-10) REVERT: A 436 TYR cc_start: 0.8215 (m-80) cc_final: 0.7835 (m-80) REVERT: A 447 LYS cc_start: 0.8243 (mttm) cc_final: 0.7973 (mttm) REVERT: A 457 ASN cc_start: 0.8371 (t0) cc_final: 0.7977 (t0) REVERT: H 36 TRP cc_start: 0.7853 (m100) cc_final: 0.7524 (m100) REVERT: H 69 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8238 (p) REVERT: H 71 THR cc_start: 0.8339 (t) cc_final: 0.8093 (p) REVERT: H 90 ASP cc_start: 0.8334 (m-30) cc_final: 0.8088 (t0) REVERT: H 91 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8112 (p) REVERT: H 114 GLN cc_start: 0.8332 (pm20) cc_final: 0.8050 (pm20) REVERT: H 119 THR cc_start: 0.7657 (OUTLIER) cc_final: 0.6980 (t) REVERT: H 145 LEU cc_start: 0.8499 (mt) cc_final: 0.8178 (mt) REVERT: H 216 LYS cc_start: 0.8714 (tppt) cc_final: 0.8452 (tppp) REVERT: H 217 LYS cc_start: 0.8742 (tttt) cc_final: 0.8499 (tttt) REVERT: L 4 LEU cc_start: 0.8680 (tp) cc_final: 0.8187 (tt) REVERT: L 18 ARG cc_start: 0.7866 (ptm-80) cc_final: 0.7604 (ptm-80) REVERT: L 22 SER cc_start: 0.8407 (p) cc_final: 0.8082 (m) REVERT: L 24 ARG cc_start: 0.7558 (ttm110) cc_final: 0.7024 (ptp-110) REVERT: L 89 GLN cc_start: 0.8178 (tt0) cc_final: 0.7870 (tt0) REVERT: L 97 MET cc_start: 0.6688 (ttm) cc_final: 0.6121 (tmm) REVERT: L 172 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6963 (p0) REVERT: L 173 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8319 (p) REVERT: L 175 TYR cc_start: 0.8206 (m-80) cc_final: 0.7843 (m-80) REVERT: L 201 GLN cc_start: 0.8280 (tt0) cc_final: 0.7948 (tt0) outliers start: 35 outliers final: 29 residues processed: 169 average time/residue: 0.1268 time to fit residues: 29.0935 Evaluate side-chains 179 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 338 TYR Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 467 CYS Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 110 ARG Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 194 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 0.0020 chunk 31 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.4326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.142116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.126423 restraints weight = 7423.362| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.80 r_work: 0.3670 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 4973 Z= 0.131 Angle : 0.666 11.931 6782 Z= 0.327 Chirality : 0.045 0.255 750 Planarity : 0.005 0.042 867 Dihedral : 6.710 52.738 699 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 6.65 % Allowed : 23.48 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.21 (0.35), residues: 619 helix: -4.67 (0.61), residues: 12 sheet: -0.69 (0.36), residues: 220 loop : -1.91 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP H 47 HIS 0.005 0.001 HIS L 191 PHE 0.023 0.002 PHE A 451 TYR 0.032 0.001 TYR A 442 ARG 0.003 0.000 ARG L 91 Details of bonding type rmsd hydrogen bonds : bond 0.02977 ( 98) hydrogen bonds : angle 5.08891 ( 240) SS BOND : bond 0.00713 ( 8) SS BOND : angle 1.84664 ( 16) covalent geometry : bond 0.00308 ( 4965) covalent geometry : angle 0.66021 ( 6766) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3100.32 seconds wall clock time: 55 minutes 47.39 seconds (3347.39 seconds total)