Starting phenix.real_space_refine on Sat May 10 03:15:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kdt_37145/05_2025/8kdt_37145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kdt_37145/05_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_37145/05_2025/8kdt_37145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kdt_37145/05_2025/8kdt_37145.map" model { file = "/net/cci-nas-00/data/ceres_data/8kdt_37145/05_2025/8kdt_37145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kdt_37145/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 3.83, per 1000 atoms: 0.79 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: 1.14 Conformation dependent library (CDL) restraints added in 597.2 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: 0.51 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: 1.15 Time building geometry restraints manager: 1.35 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: 1.970 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 15.700 Find NCS groups from input model: 0.070 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.780 ------------------------------------------------------------------------------- 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 : 0.535 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: 0.1230 time to fit residues: 32.0453 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 : 0.488 ------------------------------------------------------------------------------- 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: 0.5980 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4038 r_free = 0.4038 target = 0.146696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.130520 restraints weight = 7423.680| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.90 r_work: 0.3714 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4973 Z= 0.176 Angle : 0.637 6.585 6782 Z= 0.324 Chirality : 0.046 0.210 750 Planarity : 0.005 0.039 867 Dihedral : 6.420 48.574 708 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 6.47 % Allowed : 13.86 % Favored : 79.67 % 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: -3.64 (0.32), residues: 619 helix: -5.39 (0.31), residues: 6 sheet: -1.99 (0.34), residues: 225 loop : -2.75 (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 0.015 0.002 PHE A 360 TYR 0.022 0.002 TYR A 442 ARG 0.002 0.000 ARG L 91 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 98) hydrogen bonds : angle 6.46859 ( 240) SS BOND : bond 0.00314 ( 8) SS BOND : angle 1.55190 ( 16) covalent geometry : bond 0.00377 ( 4965) covalent geometry : angle 0.63343 ( 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 197 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7390 (m-40) cc_final: 0.7132 (m-40) REVERT: A 342 ARG cc_start: 0.8001 (ptp-110) cc_final: 0.7762 (ptp-110) REVERT: A 360 PHE cc_start: 0.6355 (OUTLIER) cc_final: 0.5748 (p90) REVERT: A 447 LYS cc_start: 0.8233 (mttm) cc_final: 0.7953 (mttm) REVERT: H 36 TRP cc_start: 0.7876 (m100) cc_final: 0.7585 (m100) REVERT: H 69 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8120 (p) REVERT: H 71 THR cc_start: 0.8426 (t) cc_final: 0.8128 (p) REVERT: H 114 GLN cc_start: 0.8353 (pt0) cc_final: 0.8125 (pm20) REVERT: H 145 LEU cc_start: 0.8361 (mt) cc_final: 0.8016 (mt) REVERT: H 187 SER cc_start: 0.8191 (t) cc_final: 0.7909 (m) REVERT: H 216 LYS cc_start: 0.8706 (tppt) cc_final: 0.8436 (tppp) REVERT: H 217 LYS cc_start: 0.8673 (tttt) cc_final: 0.8384 (tttt) REVERT: L 18 ARG cc_start: 0.7832 (ptm-80) cc_final: 0.7525 (ptm-80) REVERT: L 22 SER cc_start: 0.8381 (p) cc_final: 0.8010 (m) REVERT: L 46 LEU cc_start: 0.7767 (tp) cc_final: 0.7528 (tp) REVERT: L 138 LEU cc_start: 0.7417 (mm) cc_final: 0.7200 (mp) REVERT: L 157 GLN cc_start: 0.7467 (tp40) cc_final: 0.7157 (tp40) REVERT: L 162 GLN cc_start: 0.8472 (mt0) cc_final: 0.8251 (mt0) REVERT: L 164 SER cc_start: 0.8532 (t) cc_final: 0.7907 (p) REVERT: L 172 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7210 (p0) outliers start: 35 outliers final: 20 residues processed: 186 average time/residue: 0.1372 time to fit residues: 33.8399 Evaluate side-chains 179 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 448 LEU 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: 0.9980 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 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: 0.6980 chunk 53 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 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 473 ASN H 178 GLN L 38 GLN L 160 ASN ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.143311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.127590 restraints weight = 7474.312| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.82 r_work: 0.3685 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4973 Z= 0.181 Angle : 0.645 8.881 6782 Z= 0.324 Chirality : 0.046 0.258 750 Planarity : 0.005 0.040 867 Dihedral : 6.358 49.426 701 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 6.10 % Allowed : 18.48 % 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: -3.23 (0.33), residues: 619 helix: -5.38 (0.31), residues: 6 sheet: -1.84 (0.34), residues: 228 loop : -2.36 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 47 HIS 0.005 0.001 HIS L 90 PHE 0.016 0.002 PHE A 501 TYR 0.029 0.002 TYR A 442 ARG 0.003 0.001 ARG L 91 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 98) hydrogen bonds : angle 5.87786 ( 240) SS BOND : bond 0.01002 ( 8) SS BOND : angle 1.79473 ( 16) covalent geometry : bond 0.00401 ( 4965) covalent geometry : angle 0.63986 ( 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 192 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7440 (m-40) cc_final: 0.7200 (m-40) REVERT: A 342 ARG cc_start: 0.8046 (ptp-110) cc_final: 0.7705 (ptp-170) REVERT: A 360 PHE cc_start: 0.6422 (OUTLIER) cc_final: 0.5854 (p90) REVERT: A 447 LYS cc_start: 0.8281 (mttm) cc_final: 0.8024 (mttm) REVERT: A 457 ASN cc_start: 0.8343 (t0) cc_final: 0.8087 (t0) REVERT: H 36 TRP cc_start: 0.7873 (m100) cc_final: 0.7529 (m100) REVERT: H 69 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8145 (p) REVERT: H 71 THR cc_start: 0.8383 (t) cc_final: 0.8111 (p) REVERT: H 90 ASP cc_start: 0.8399 (m-30) cc_final: 0.8128 (t0) REVERT: H 114 GLN cc_start: 0.8376 (pt0) cc_final: 0.8166 (pm20) REVERT: H 129 PHE cc_start: 0.7972 (m-10) cc_final: 0.7720 (m-10) REVERT: H 145 LEU cc_start: 0.8398 (mt) cc_final: 0.8129 (mt) REVERT: H 183 TYR cc_start: 0.8190 (m-10) cc_final: 0.7844 (m-10) REVERT: H 187 SER cc_start: 0.8296 (t) cc_final: 0.7966 (m) REVERT: H 188 VAL cc_start: 0.8642 (t) cc_final: 0.8385 (p) REVERT: H 216 LYS cc_start: 0.8731 (tppt) cc_final: 0.8475 (tppp) REVERT: H 217 LYS cc_start: 0.8671 (tttt) cc_final: 0.8385 (tttt) REVERT: L 18 ARG cc_start: 0.7807 (ptm-80) cc_final: 0.7507 (ptm-80) REVERT: L 22 SER cc_start: 0.8406 (p) cc_final: 0.8080 (m) REVERT: L 46 LEU cc_start: 0.7859 (tp) cc_final: 0.7617 (tp) REVERT: L 164 SER cc_start: 0.8547 (t) cc_final: 0.8007 (p) REVERT: L 175 TYR cc_start: 0.7989 (m-80) cc_final: 0.7370 (m-80) outliers start: 33 outliers final: 23 residues processed: 181 average time/residue: 0.1258 time to fit residues: 30.6586 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 : 0.530 ------------------------------------------------------------------------------- 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 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 26 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 173 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 49 optimal weight: 0.6980 chunk 41 optimal weight: 0.0270 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.0270 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.144645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.128603 restraints weight = 7537.703| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.92 r_work: 0.3697 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2959 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= 0.125 Angle : 0.627 8.885 6782 Z= 0.308 Chirality : 0.044 0.228 750 Planarity : 0.005 0.038 867 Dihedral : 6.309 49.187 701 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 5.18 % Allowed : 20.89 % Favored : 73.94 % 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: -3.05 (0.33), residues: 619 helix: -5.38 (0.31), residues: 6 sheet: -1.62 (0.33), residues: 238 loop : -2.30 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 47 HIS 0.003 0.001 HIS L 191 PHE 0.021 0.002 PHE A 379 TYR 0.028 0.002 TYR A 442 ARG 0.002 0.000 ARG L 91 Details of bonding type rmsd hydrogen bonds : bond 0.03001 ( 98) hydrogen bonds : angle 5.52835 ( 240) SS BOND : bond 0.00637 ( 8) SS BOND : angle 1.78360 ( 16) covalent geometry : bond 0.00289 ( 4965) covalent geometry : angle 0.62194 ( 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 182 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7410 (m-40) cc_final: 0.7172 (m-40) REVERT: A 379 PHE cc_start: 0.7288 (m-80) cc_final: 0.7004 (m-10) REVERT: A 447 LYS cc_start: 0.8191 (mttm) cc_final: 0.7911 (mttm) REVERT: A 457 ASN cc_start: 0.8328 (t0) cc_final: 0.8092 (t0) REVERT: H 36 TRP cc_start: 0.7876 (m100) cc_final: 0.7510 (m100) REVERT: H 69 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8143 (p) REVERT: H 71 THR cc_start: 0.8351 (t) cc_final: 0.8065 (p) REVERT: H 90 ASP cc_start: 0.8378 (m-30) cc_final: 0.8072 (t0) REVERT: H 91 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.8053 (p) REVERT: H 114 GLN cc_start: 0.8367 (pt0) cc_final: 0.8108 (pm20) REVERT: H 145 LEU cc_start: 0.8380 (mt) cc_final: 0.8127 (mt) REVERT: H 183 TYR cc_start: 0.8234 (m-10) cc_final: 0.7869 (m-10) REVERT: H 187 SER cc_start: 0.8347 (t) cc_final: 0.7997 (m) REVERT: H 188 VAL cc_start: 0.8578 (t) cc_final: 0.8312 (p) REVERT: H 216 LYS cc_start: 0.8697 (tppt) cc_final: 0.8431 (tppp) REVERT: H 217 LYS cc_start: 0.8665 (tttt) cc_final: 0.8375 (tttt) REVERT: L 18 ARG cc_start: 0.7848 (ptm-80) cc_final: 0.7543 (ptm-80) REVERT: L 22 SER cc_start: 0.8401 (p) cc_final: 0.8051 (m) REVERT: L 162 GLN cc_start: 0.8539 (mt0) cc_final: 0.8227 (mt0) REVERT: L 164 SER cc_start: 0.8528 (t) cc_final: 0.7992 (p) REVERT: L 172 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7171 (p0) REVERT: L 175 TYR cc_start: 0.8008 (m-80) cc_final: 0.7378 (m-80) outliers start: 28 outliers final: 21 residues processed: 172 average time/residue: 0.1291 time to fit residues: 30.0898 Evaluate side-chains 177 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 478 LEU 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 123 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3988 r_free = 0.3988 target = 0.141764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.125786 restraints weight = 7598.555| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.90 r_work: 0.3664 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4973 Z= 0.175 Angle : 0.660 11.007 6782 Z= 0.326 Chirality : 0.045 0.246 750 Planarity : 0.005 0.038 867 Dihedral : 6.484 50.076 700 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 6.84 % Allowed : 19.78 % Favored : 73.38 % 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: -2.82 (0.33), residues: 619 helix: -5.37 (0.30), residues: 6 sheet: -1.31 (0.34), residues: 215 loop : -2.24 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 47 HIS 0.004 0.001 HIS L 191 PHE 0.014 0.002 PHE A 360 TYR 0.032 0.002 TYR A 442 ARG 0.002 0.000 ARG L 91 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 98) hydrogen bonds : angle 5.35760 ( 240) SS BOND : bond 0.00477 ( 8) SS BOND : angle 1.83810 ( 16) covalent geometry : bond 0.00391 ( 4965) covalent geometry : angle 0.65507 ( 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 190 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7427 (m-40) cc_final: 0.7187 (m-40) REVERT: A 342 ARG cc_start: 0.8066 (ptp-110) cc_final: 0.7296 (ptp-110) REVERT: A 360 PHE cc_start: 0.6266 (OUTLIER) cc_final: 0.5761 (p90) REVERT: A 383 TYR cc_start: 0.8018 (m-10) cc_final: 0.7429 (m-80) REVERT: A 447 LYS cc_start: 0.8274 (mttm) cc_final: 0.8009 (mttm) REVERT: A 451 PHE cc_start: 0.7830 (m-10) cc_final: 0.7567 (m-10) REVERT: A 457 ASN cc_start: 0.8344 (t0) cc_final: 0.8020 (t0) REVERT: A 501 PHE cc_start: 0.7869 (m-80) cc_final: 0.7653 (m-80) REVERT: H 36 TRP cc_start: 0.7853 (m100) cc_final: 0.7507 (m100) REVERT: H 69 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8205 (p) REVERT: H 71 THR cc_start: 0.8352 (t) cc_final: 0.8084 (p) REVERT: H 90 ASP cc_start: 0.8365 (m-30) cc_final: 0.8055 (t0) REVERT: H 114 GLN cc_start: 0.8418 (pt0) cc_final: 0.8130 (pm20) REVERT: H 145 LEU cc_start: 0.8451 (mt) cc_final: 0.8203 (mt) REVERT: H 183 TYR cc_start: 0.8364 (m-10) cc_final: 0.8049 (m-10) REVERT: H 188 VAL cc_start: 0.8608 (t) cc_final: 0.8334 (p) REVERT: H 216 LYS cc_start: 0.8745 (tppt) cc_final: 0.8477 (tppp) REVERT: H 217 LYS cc_start: 0.8723 (tttt) cc_final: 0.8447 (tttt) REVERT: L 18 ARG cc_start: 0.7803 (ptm-80) cc_final: 0.7529 (ptm-80) REVERT: L 22 SER cc_start: 0.8410 (p) cc_final: 0.8060 (m) REVERT: L 46 LEU cc_start: 0.7816 (tp) cc_final: 0.7607 (tp) REVERT: L 97 MET cc_start: 0.7288 (ttm) cc_final: 0.7074 (ttm) REVERT: L 164 SER cc_start: 0.8549 (t) cc_final: 0.8063 (p) REVERT: L 172 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7033 (p0) REVERT: L 173 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.8207 (p) REVERT: L 175 TYR cc_start: 0.8116 (m-80) cc_final: 0.7648 (m-80) outliers start: 37 outliers final: 28 residues processed: 176 average time/residue: 0.1263 time to fit residues: 29.9715 Evaluate side-chains 184 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 360 PHE 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 496 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 120 VAL Chi-restraints excluded: chain H residue 123 THR 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 147 LYS Chi-restraints excluded: chain L residue 152 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 43 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.0270 chunk 35 optimal weight: 5.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.142925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.126997 restraints weight = 7458.331| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.86 r_work: 0.3680 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3463 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= 0.138 Angle : 0.639 10.605 6782 Z= 0.314 Chirality : 0.045 0.265 750 Planarity : 0.005 0.041 867 Dihedral : 6.481 50.044 700 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 6.65 % Allowed : 20.15 % Favored : 73.20 % 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: -2.71 (0.34), residues: 619 helix: -5.38 (0.30), residues: 6 sheet: -1.23 (0.33), residues: 228 loop : -2.19 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 47 HIS 0.003 0.001 HIS L 191 PHE 0.019 0.002 PHE A 379 TYR 0.030 0.002 TYR A 442 ARG 0.002 0.000 ARG L 91 Details of bonding type rmsd hydrogen bonds : bond 0.03015 ( 98) hydrogen bonds : angle 5.36908 ( 240) SS BOND : bond 0.00725 ( 8) SS BOND : angle 1.86012 ( 16) covalent geometry : bond 0.00325 ( 4965) covalent geometry : angle 0.63314 ( 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 189 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 153 time to evaluate : 0.590 Fit side-chains REVERT: A 330 ASN cc_start: 0.7391 (m-40) cc_final: 0.7142 (m-40) REVERT: A 383 TYR cc_start: 0.7959 (m-10) cc_final: 0.7438 (m-80) REVERT: A 447 LYS cc_start: 0.8205 (mttm) cc_final: 0.7923 (mttm) REVERT: A 451 PHE cc_start: 0.7756 (m-10) cc_final: 0.7531 (m-10) REVERT: A 457 ASN cc_start: 0.8344 (t0) cc_final: 0.8000 (t0) REVERT: H 36 TRP cc_start: 0.7864 (m100) cc_final: 0.7513 (m100) REVERT: H 69 THR cc_start: 0.8499 (OUTLIER) cc_final: 0.8183 (p) REVERT: H 71 THR cc_start: 0.8318 (t) cc_final: 0.8058 (p) REVERT: H 90 ASP cc_start: 0.8320 (m-30) cc_final: 0.8020 (t0) REVERT: H 91 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.8087 (p) REVERT: H 114 GLN cc_start: 0.8367 (pt0) cc_final: 0.8105 (pm20) REVERT: H 145 LEU cc_start: 0.8478 (mt) cc_final: 0.8168 (mt) REVERT: H 183 TYR cc_start: 0.8341 (m-10) cc_final: 0.8065 (m-10) REVERT: H 216 LYS cc_start: 0.8734 (tppt) cc_final: 0.8469 (tppp) REVERT: H 217 LYS cc_start: 0.8698 (tttt) cc_final: 0.8425 (tttt) REVERT: L 18 ARG cc_start: 0.7864 (ptm-80) cc_final: 0.7570 (ptm-80) REVERT: L 22 SER cc_start: 0.8391 (p) cc_final: 0.8035 (m) REVERT: L 164 SER cc_start: 0.8505 (t) cc_final: 0.8037 (p) REVERT: L 172 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7064 (p0) REVERT: L 173 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8236 (p) REVERT: L 175 TYR cc_start: 0.8102 (m-80) cc_final: 0.7651 (m-80) REVERT: L 178 SER cc_start: 0.8446 (t) cc_final: 0.8172 (t) outliers start: 36 outliers final: 29 residues processed: 176 average time/residue: 0.1328 time to fit residues: 32.0553 Evaluate side-chains 185 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 467 CYS Chi-restraints excluded: chain A residue 478 LEU 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 96 CYS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 123 THR 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 111 THR Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 147 LYS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 44 optimal weight: 0.0010 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 0.2980 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.142541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.126755 restraints weight = 7365.909| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.84 r_work: 0.3671 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 4973 Z= 0.149 Angle : 0.650 11.793 6782 Z= 0.321 Chirality : 0.045 0.277 750 Planarity : 0.005 0.038 867 Dihedral : 6.545 50.510 700 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 7.02 % Allowed : 20.70 % 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: -2.66 (0.34), residues: 619 helix: -4.80 (0.44), residues: 12 sheet: -1.11 (0.34), residues: 226 loop : -2.17 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 47 HIS 0.004 0.001 HIS L 191 PHE 0.027 0.002 PHE A 416 TYR 0.031 0.002 TYR A 442 ARG 0.002 0.000 ARG L 91 Details of bonding type rmsd hydrogen bonds : bond 0.03059 ( 98) hydrogen bonds : angle 5.30198 ( 240) SS BOND : bond 0.00696 ( 8) SS BOND : angle 1.96096 ( 16) covalent geometry : bond 0.00345 ( 4965) covalent geometry : angle 0.64419 ( 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 191 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7345 (m-40) cc_final: 0.7114 (m-40) REVERT: A 334 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7115 (m-10) REVERT: A 383 TYR cc_start: 0.7962 (m-10) cc_final: 0.7432 (m-80) REVERT: A 447 LYS cc_start: 0.8208 (mttm) cc_final: 0.7916 (mttm) REVERT: A 451 PHE cc_start: 0.7716 (m-10) cc_final: 0.7498 (m-10) REVERT: A 457 ASN cc_start: 0.8388 (t0) cc_final: 0.8011 (t0) REVERT: H 36 TRP cc_start: 0.7860 (m100) cc_final: 0.7540 (m100) REVERT: H 69 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8193 (p) REVERT: H 71 THR cc_start: 0.8318 (t) cc_final: 0.8065 (p) REVERT: H 90 ASP cc_start: 0.8305 (m-30) cc_final: 0.7965 (m-30) REVERT: H 91 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.8117 (p) REVERT: H 114 GLN cc_start: 0.8366 (pt0) cc_final: 0.8126 (pm20) REVERT: H 145 LEU cc_start: 0.8463 (mt) cc_final: 0.8131 (mt) REVERT: H 183 TYR cc_start: 0.8374 (m-10) cc_final: 0.8050 (m-10) REVERT: H 216 LYS cc_start: 0.8743 (tppt) cc_final: 0.8484 (tppp) REVERT: H 217 LYS cc_start: 0.8725 (tttt) cc_final: 0.8464 (tttt) REVERT: L 18 ARG cc_start: 0.7819 (ptm-80) cc_final: 0.7568 (ptm-80) REVERT: L 22 SER cc_start: 0.8381 (p) cc_final: 0.8042 (m) REVERT: L 46 LEU cc_start: 0.7785 (tp) cc_final: 0.7583 (tp) REVERT: L 164 SER cc_start: 0.8473 (t) cc_final: 0.7961 (p) REVERT: L 172 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.7008 (p0) REVERT: L 173 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8269 (p) REVERT: L 175 TYR cc_start: 0.8133 (m-80) cc_final: 0.7664 (m-80) outliers start: 38 outliers final: 29 residues processed: 178 average time/residue: 0.1203 time to fit residues: 29.2210 Evaluate side-chains 184 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 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 96 CYS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 123 THR 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 45 optimal weight: 0.0060 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.0370 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 overall best weight: 0.4674 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.142987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.127177 restraints weight = 7465.338| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.85 r_work: 0.3682 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 4973 Z= 0.131 Angle : 0.653 12.567 6782 Z= 0.319 Chirality : 0.045 0.266 750 Planarity : 0.005 0.040 867 Dihedral : 6.575 50.346 700 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 6.47 % Allowed : 21.81 % 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: -2.50 (0.34), residues: 619 helix: -4.85 (0.44), residues: 12 sheet: -1.02 (0.34), residues: 226 loop : -2.03 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 47 HIS 0.005 0.001 HIS L 191 PHE 0.030 0.002 PHE A 416 TYR 0.031 0.001 TYR A 442 ARG 0.003 0.000 ARG L 91 Details of bonding type rmsd hydrogen bonds : bond 0.02914 ( 98) hydrogen bonds : angle 5.15178 ( 240) SS BOND : bond 0.00601 ( 8) SS BOND : angle 1.94756 ( 16) covalent geometry : bond 0.00310 ( 4965) covalent geometry : angle 0.64656 ( 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 185 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7362 (m-40) cc_final: 0.7141 (m-40) REVERT: A 383 TYR cc_start: 0.7955 (m-10) cc_final: 0.7510 (m-80) REVERT: A 447 LYS cc_start: 0.8200 (mttm) cc_final: 0.7940 (mttm) REVERT: A 451 PHE cc_start: 0.7679 (m-10) cc_final: 0.7463 (m-10) REVERT: A 457 ASN cc_start: 0.8370 (t0) cc_final: 0.7988 (t0) REVERT: H 36 TRP cc_start: 0.7877 (m100) cc_final: 0.7569 (m100) REVERT: H 69 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8203 (p) REVERT: H 71 THR cc_start: 0.8314 (t) cc_final: 0.8064 (p) REVERT: H 90 ASP cc_start: 0.8302 (m-30) cc_final: 0.7968 (m-30) REVERT: H 91 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.8098 (p) REVERT: H 114 GLN cc_start: 0.8340 (pt0) cc_final: 0.8093 (pm20) REVERT: H 145 LEU cc_start: 0.8475 (mt) cc_final: 0.8157 (mt) REVERT: H 183 TYR cc_start: 0.8380 (m-10) cc_final: 0.8118 (m-10) REVERT: H 216 LYS cc_start: 0.8726 (tppt) cc_final: 0.8474 (tppp) REVERT: H 217 LYS cc_start: 0.8703 (tttt) cc_final: 0.8440 (tttt) REVERT: L 18 ARG cc_start: 0.7827 (ptm-80) cc_final: 0.7568 (ptm-80) REVERT: L 22 SER cc_start: 0.8381 (p) cc_final: 0.8021 (m) REVERT: L 46 LEU cc_start: 0.7781 (tp) cc_final: 0.7580 (tp) REVERT: L 164 SER cc_start: 0.8481 (t) cc_final: 0.7948 (p) REVERT: L 172 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.6994 (p0) REVERT: L 173 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8284 (p) REVERT: L 175 TYR cc_start: 0.8125 (m-80) cc_final: 0.7688 (m-80) outliers start: 35 outliers final: 28 residues processed: 173 average time/residue: 0.1159 time to fit residues: 27.3578 Evaluate side-chains 182 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 467 CYS Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 502 GLU 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 120 VAL 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 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 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: 3.9990 chunk 24 optimal weight: 0.6980 chunk 56 optimal weight: 0.0170 chunk 30 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.142511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.126814 restraints weight = 7395.503| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.84 r_work: 0.3680 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3856 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= 0.133 Angle : 0.662 11.973 6782 Z= 0.324 Chirality : 0.045 0.259 750 Planarity : 0.005 0.038 867 Dihedral : 6.617 50.919 700 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 6.65 % Allowed : 22.55 % 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: -2.42 (0.34), residues: 619 helix: -5.28 (0.20), residues: 12 sheet: -0.98 (0.34), residues: 226 loop : -1.94 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 47 HIS 0.004 0.001 HIS L 191 PHE 0.033 0.002 PHE A 416 TYR 0.031 0.001 TYR A 442 ARG 0.002 0.000 ARG L 91 Details of bonding type rmsd hydrogen bonds : bond 0.02920 ( 98) hydrogen bonds : angle 5.17261 ( 240) SS BOND : bond 0.00733 ( 8) SS BOND : angle 1.88188 ( 16) covalent geometry : bond 0.00312 ( 4965) covalent geometry : angle 0.65621 ( 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 187 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7380 (m-40) cc_final: 0.7158 (m-40) REVERT: A 334 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7151 (m-10) REVERT: A 447 LYS cc_start: 0.8189 (mttm) cc_final: 0.7915 (mttm) REVERT: A 451 PHE cc_start: 0.7668 (m-10) cc_final: 0.7416 (m-10) REVERT: A 457 ASN cc_start: 0.8363 (t0) cc_final: 0.7971 (t0) REVERT: H 36 TRP cc_start: 0.7881 (m100) cc_final: 0.7563 (m100) REVERT: H 69 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8215 (p) REVERT: H 71 THR cc_start: 0.8338 (t) cc_final: 0.8086 (p) REVERT: H 90 ASP cc_start: 0.8313 (m-30) cc_final: 0.7996 (m-30) REVERT: H 114 GLN cc_start: 0.8335 (pt0) cc_final: 0.8101 (pm20) REVERT: H 145 LEU cc_start: 0.8476 (mt) cc_final: 0.8157 (mt) REVERT: H 183 TYR cc_start: 0.8411 (m-10) cc_final: 0.8143 (m-10) REVERT: H 216 LYS cc_start: 0.8723 (tppt) cc_final: 0.8474 (tppp) REVERT: H 217 LYS cc_start: 0.8710 (tttt) cc_final: 0.8455 (tttt) REVERT: L 18 ARG cc_start: 0.7808 (ptm-80) cc_final: 0.7546 (ptm-80) REVERT: L 22 SER cc_start: 0.8367 (p) cc_final: 0.8035 (m) REVERT: L 46 LEU cc_start: 0.7787 (tp) cc_final: 0.7579 (tp) REVERT: L 97 MET cc_start: 0.6504 (ttm) cc_final: 0.6284 (tmm) REVERT: L 164 SER cc_start: 0.8496 (t) cc_final: 0.7956 (p) REVERT: L 172 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6994 (p0) REVERT: L 173 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8284 (p) REVERT: L 175 TYR cc_start: 0.8123 (m-80) cc_final: 0.7695 (m-80) outliers start: 36 outliers final: 26 residues processed: 174 average time/residue: 0.1204 time to fit residues: 28.6181 Evaluate side-chains 189 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 502 GLU 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 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 120 VAL Chi-restraints excluded: chain H residue 123 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.142659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.127294 restraints weight = 7513.383| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.72 r_work: 0.3693 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3949 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= 0.133 Angle : 0.668 12.576 6782 Z= 0.330 Chirality : 0.045 0.255 750 Planarity : 0.005 0.040 867 Dihedral : 6.632 51.484 699 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 5.91 % Allowed : 22.92 % Favored : 71.16 % 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: -2.33 (0.34), residues: 619 helix: -5.35 (0.18), residues: 12 sheet: -0.93 (0.35), residues: 226 loop : -1.86 (0.33), residues: 381 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 0.033 0.002 PHE A 416 TYR 0.031 0.001 TYR A 442 ARG 0.003 0.000 ARG L 91 Details of bonding type rmsd hydrogen bonds : bond 0.02995 ( 98) hydrogen bonds : angle 5.22994 ( 240) SS BOND : bond 0.00647 ( 8) SS BOND : angle 1.87936 ( 16) covalent geometry : bond 0.00313 ( 4965) covalent geometry : angle 0.66221 ( 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 191 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7389 (m-40) cc_final: 0.7185 (m-40) REVERT: A 334 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7158 (m-10) REVERT: A 447 LYS cc_start: 0.8162 (mttm) cc_final: 0.7877 (mttm) REVERT: A 451 PHE cc_start: 0.7691 (m-10) cc_final: 0.7442 (m-10) REVERT: A 457 ASN cc_start: 0.8350 (t0) cc_final: 0.7969 (t0) REVERT: H 36 TRP cc_start: 0.7885 (m100) cc_final: 0.7632 (m100) REVERT: H 69 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8251 (p) REVERT: H 90 ASP cc_start: 0.8229 (m-30) cc_final: 0.7899 (m-30) REVERT: H 116 THR cc_start: 0.8616 (m) cc_final: 0.8121 (p) REVERT: H 145 LEU cc_start: 0.8496 (mt) cc_final: 0.8192 (mt) REVERT: H 216 LYS cc_start: 0.8682 (tppt) cc_final: 0.8457 (tppp) REVERT: H 217 LYS cc_start: 0.8641 (tttt) cc_final: 0.8404 (tttt) REVERT: L 18 ARG cc_start: 0.7763 (ptm-80) cc_final: 0.7548 (ptm-80) REVERT: L 22 SER cc_start: 0.8362 (p) cc_final: 0.8029 (m) REVERT: L 46 LEU cc_start: 0.7742 (tp) cc_final: 0.7542 (tp) REVERT: L 97 MET cc_start: 0.6459 (ttm) cc_final: 0.6247 (tmm) REVERT: L 160 ASN cc_start: 0.7766 (p0) cc_final: 0.7488 (p0) REVERT: L 164 SER cc_start: 0.8460 (t) cc_final: 0.7947 (p) REVERT: L 172 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.6976 (p0) REVERT: L 173 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8296 (p) REVERT: L 175 TYR cc_start: 0.8142 (m-80) cc_final: 0.7755 (m-80) REVERT: L 209 LYS cc_start: 0.7248 (mmtt) cc_final: 0.7034 (mmtt) outliers start: 32 outliers final: 25 residues processed: 176 average time/residue: 0.1161 time to fit residues: 28.0219 Evaluate side-chains 188 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 502 GLU 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 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 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 171 LYS Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 173 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 12 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.0770 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.143603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.128282 restraints weight = 7430.961| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.71 r_work: 0.3699 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.4021 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= 0.121 Angle : 0.650 12.132 6782 Z= 0.322 Chirality : 0.045 0.244 750 Planarity : 0.005 0.040 867 Dihedral : 6.593 51.496 699 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 5.36 % Allowed : 23.84 % 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: -2.05 (0.35), residues: 619 helix: -5.37 (0.30), residues: 6 sheet: -0.67 (0.35), residues: 223 loop : -1.79 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 47 HIS 0.004 0.001 HIS L 191 PHE 0.024 0.002 PHE A 416 TYR 0.031 0.001 TYR A 442 ARG 0.003 0.000 ARG L 91 Details of bonding type rmsd hydrogen bonds : bond 0.02870 ( 98) hydrogen bonds : angle 5.16992 ( 240) SS BOND : bond 0.00725 ( 8) SS BOND : angle 1.82615 ( 16) covalent geometry : bond 0.00286 ( 4965) covalent geometry : angle 0.64473 ( 6766) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2917.77 seconds wall clock time: 51 minutes 20.81 seconds (3080.81 seconds total)