Starting phenix.real_space_refine on Fri Aug 22 15:19:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kdt_37145/08_2025/8kdt_37145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kdt_37145/08_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_37145/08_2025/8kdt_37145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kdt_37145/08_2025/8kdt_37145.map" model { file = "/net/cci-nas-00/data/ceres_data/8kdt_37145/08_2025/8kdt_37145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kdt_37145/08_2025/8kdt_37145.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.34, per 1000 atoms: 0.28 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: 0.39 Conformation dependent library (CDL) restraints added in 184.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.12 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: 0.55 Time building geometry restraints manager: 0.54 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: 1.900 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.900 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.830 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.001 0.000 ARG L 54 TYR 0.006 0.001 TYR L 49 PHE 0.009 0.001 PHE A 360 TRP 0.023 0.001 TRP H 47 HIS 0.001 0.000 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 4965) covalent geometry : angle 0.51451 ( 6766) SS BOND : bond 0.00130 ( 8) SS BOND : angle 0.42018 ( 16) hydrogen bonds : bond 0.30134 ( 98) hydrogen bonds : angle 10.56742 ( 240) *********************** 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 : 0.112 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: 0.0452 time to fit residues: 12.0812 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 : 0.131 ------------------------------------------------------------------------------- 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 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.0050 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.147026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.130924 restraints weight = 7475.732| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.88 r_work: 0.3722 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4973 Z= 0.153 Angle : 0.623 6.459 6782 Z= 0.315 Chirality : 0.045 0.171 750 Planarity : 0.005 0.039 867 Dihedral : 6.355 48.445 708 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.61 (0.32), residues: 619 helix: -5.39 (0.31), residues: 6 sheet: -1.96 (0.34), residues: 225 loop : -2.74 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 91 TYR 0.024 0.002 TYR A 442 PHE 0.013 0.002 PHE A 360 TRP 0.028 0.002 TRP H 47 HIS 0.005 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 4965) covalent geometry : angle 0.61960 ( 6766) SS BOND : bond 0.00484 ( 8) SS BOND : angle 1.52956 ( 16) hydrogen bonds : bond 0.04201 ( 98) hydrogen bonds : angle 6.45889 ( 240) *********************** 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 192 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 ARG cc_start: 0.7964 (ptp-110) cc_final: 0.7734 (ptp-110) REVERT: A 360 PHE cc_start: 0.6322 (OUTLIER) cc_final: 0.5700 (p90) REVERT: A 447 LYS cc_start: 0.8199 (mttm) cc_final: 0.7900 (mttm) REVERT: H 36 TRP cc_start: 0.7854 (m100) cc_final: 0.7568 (m100) REVERT: H 69 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8102 (p) REVERT: H 71 THR cc_start: 0.8393 (t) cc_final: 0.8094 (p) REVERT: H 145 LEU cc_start: 0.8377 (mt) cc_final: 0.8046 (mt) REVERT: H 187 SER cc_start: 0.8178 (t) cc_final: 0.7904 (m) REVERT: H 216 LYS cc_start: 0.8700 (tppt) cc_final: 0.8441 (tppp) REVERT: H 217 LYS cc_start: 0.8679 (tttt) cc_final: 0.8396 (tttt) REVERT: L 18 ARG cc_start: 0.7871 (ptm-80) cc_final: 0.7544 (ptm-80) REVERT: L 22 SER cc_start: 0.8353 (p) cc_final: 0.7975 (m) REVERT: L 46 LEU cc_start: 0.7752 (tp) cc_final: 0.7520 (tp) REVERT: L 138 LEU cc_start: 0.7425 (mm) cc_final: 0.7211 (mp) REVERT: L 157 GLN cc_start: 0.7486 (tp40) cc_final: 0.7160 (tp40) REVERT: L 162 GLN cc_start: 0.8467 (mt0) cc_final: 0.8239 (mt0) REVERT: L 164 SER cc_start: 0.8534 (t) cc_final: 0.7928 (p) REVERT: L 172 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7183 (p0) outliers start: 34 outliers final: 20 residues processed: 181 average time/residue: 0.0488 time to fit residues: 11.8487 Evaluate side-chains 177 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 382 VAL 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 57 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 44 optimal weight: 0.0470 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 58 optimal weight: 0.0370 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN L 38 GLN L 160 ASN L 191 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.146207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.130278 restraints weight = 7371.049| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.83 r_work: 0.3727 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2565 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= 0.128 Angle : 0.608 8.857 6782 Z= 0.302 Chirality : 0.045 0.245 750 Planarity : 0.005 0.038 867 Dihedral : 6.089 48.936 701 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 5.73 % Allowed : 18.48 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.14 (0.33), residues: 619 helix: -5.38 (0.31), residues: 6 sheet: -1.48 (0.36), residues: 218 loop : -2.52 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 91 TYR 0.029 0.001 TYR A 442 PHE 0.015 0.002 PHE A 451 TRP 0.027 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4965) covalent geometry : angle 0.60214 ( 6766) SS BOND : bond 0.00669 ( 8) SS BOND : angle 1.77089 ( 16) hydrogen bonds : bond 0.03365 ( 98) hydrogen bonds : angle 5.81466 ( 240) *********************** 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 185 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 447 LYS cc_start: 0.8191 (mttm) cc_final: 0.7907 (mttm) REVERT: H 36 TRP cc_start: 0.7866 (m100) cc_final: 0.7492 (m100) REVERT: H 69 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8133 (p) REVERT: H 71 THR cc_start: 0.8329 (t) cc_final: 0.8033 (p) REVERT: H 91 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7965 (p) REVERT: H 145 LEU cc_start: 0.8345 (mt) cc_final: 0.7997 (mt) REVERT: H 187 SER cc_start: 0.8290 (t) cc_final: 0.7974 (m) REVERT: H 188 VAL cc_start: 0.8578 (t) cc_final: 0.8312 (p) REVERT: H 216 LYS cc_start: 0.8706 (tppt) cc_final: 0.8441 (tppp) REVERT: H 217 LYS cc_start: 0.8662 (tttt) cc_final: 0.8378 (tttt) REVERT: L 18 ARG cc_start: 0.7822 (ptm-80) cc_final: 0.7512 (ptm-80) REVERT: L 22 SER cc_start: 0.8366 (p) cc_final: 0.8010 (m) REVERT: L 46 LEU cc_start: 0.7769 (tp) cc_final: 0.7543 (tp) REVERT: L 162 GLN cc_start: 0.8463 (mt0) cc_final: 0.8234 (mt0) REVERT: L 164 SER cc_start: 0.8543 (t) cc_final: 0.8017 (p) REVERT: L 175 TYR cc_start: 0.7862 (m-80) cc_final: 0.7132 (m-80) outliers start: 31 outliers final: 22 residues processed: 174 average time/residue: 0.0473 time to fit residues: 11.3888 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 : 0.120 ------------------------------------------------------------------------------- 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 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 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 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 20 optimal weight: 0.0870 chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.144729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.129399 restraints weight = 7482.381| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.71 r_work: 0.3717 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 4973 Z= 0.141 Angle : 0.615 8.817 6782 Z= 0.305 Chirality : 0.044 0.251 750 Planarity : 0.005 0.037 867 Dihedral : 6.239 49.145 701 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 6.28 % Allowed : 18.48 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.95 (0.33), residues: 619 helix: -5.38 (0.31), residues: 6 sheet: -1.51 (0.34), residues: 228 loop : -2.27 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 91 TYR 0.030 0.002 TYR A 442 PHE 0.017 0.002 PHE A 416 TRP 0.028 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4965) covalent geometry : angle 0.60953 ( 6766) SS BOND : bond 0.00457 ( 8) SS BOND : angle 1.77348 ( 16) hydrogen bonds : bond 0.03116 ( 98) hydrogen bonds : angle 5.39369 ( 240) *********************** 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: 34 poor density : 159 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7409 (m-40) cc_final: 0.7197 (m-40) REVERT: A 379 PHE cc_start: 0.7597 (m-80) cc_final: 0.7383 (m-10) REVERT: A 447 LYS cc_start: 0.8126 (mttm) cc_final: 0.7875 (mttm) REVERT: A 451 PHE cc_start: 0.7864 (m-10) cc_final: 0.7663 (m-10) REVERT: A 457 ASN cc_start: 0.8274 (t0) cc_final: 0.8066 (t0) REVERT: A 501 PHE cc_start: 0.7895 (m-80) cc_final: 0.7639 (m-80) REVERT: H 36 TRP cc_start: 0.7845 (m100) cc_final: 0.7597 (m100) REVERT: H 69 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.8211 (p) REVERT: H 71 THR cc_start: 0.8367 (t) cc_final: 0.8097 (p) REVERT: H 90 ASP cc_start: 0.8263 (m-30) cc_final: 0.8018 (t0) REVERT: H 91 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.7978 (p) REVERT: H 145 LEU cc_start: 0.8449 (mt) cc_final: 0.8187 (mt) REVERT: H 188 VAL cc_start: 0.8563 (t) cc_final: 0.8308 (p) REVERT: H 216 LYS cc_start: 0.8634 (tppt) cc_final: 0.8419 (tppp) REVERT: H 217 LYS cc_start: 0.8585 (tttt) cc_final: 0.8326 (tttt) REVERT: L 18 ARG cc_start: 0.7765 (ptm-80) cc_final: 0.7501 (ptm-80) REVERT: L 22 SER cc_start: 0.8364 (p) cc_final: 0.8062 (m) REVERT: L 46 LEU cc_start: 0.7728 (tp) cc_final: 0.7482 (tp) REVERT: L 162 GLN cc_start: 0.8549 (mt0) cc_final: 0.8245 (mt0) REVERT: L 164 SER cc_start: 0.8492 (t) cc_final: 0.8039 (p) REVERT: L 172 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7091 (p0) REVERT: L 175 TYR cc_start: 0.7961 (m-80) cc_final: 0.7415 (m-80) outliers start: 34 outliers final: 25 residues processed: 180 average time/residue: 0.0457 time to fit residues: 11.3926 Evaluate side-chains 184 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.107 ------------------------------------------------------------------------------- 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 48 MET 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 99 THR Chi-restraints excluded: chain L residue 109 LYS 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 171 LYS Chi-restraints excluded: chain L residue 172 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 56 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.139570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.123393 restraints weight = 7547.437| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.89 r_work: 0.3626 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 4973 Z= 0.253 Angle : 0.704 9.467 6782 Z= 0.356 Chirality : 0.047 0.284 750 Planarity : 0.005 0.043 867 Dihedral : 6.773 50.488 701 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 6.28 % Allowed : 20.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.96 (0.33), residues: 619 helix: -5.07 (0.29), residues: 12 sheet: -1.28 (0.35), residues: 215 loop : -2.38 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 91 TYR 0.033 0.002 TYR A 442 PHE 0.020 0.002 PHE A 360 TRP 0.031 0.002 TRP H 47 HIS 0.004 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 4965) covalent geometry : angle 0.69855 ( 6766) SS BOND : bond 0.00893 ( 8) SS BOND : angle 1.97488 ( 16) hydrogen bonds : bond 0.03757 ( 98) hydrogen bonds : angle 5.62617 ( 240) *********************** 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 192 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7374 (m-40) cc_final: 0.7146 (m-40) REVERT: A 342 ARG cc_start: 0.8088 (ptp-110) cc_final: 0.7250 (ptp-110) REVERT: A 379 PHE cc_start: 0.7661 (m-80) cc_final: 0.7376 (m-10) REVERT: A 436 TYR cc_start: 0.8228 (m-80) cc_final: 0.7968 (m-80) REVERT: A 447 LYS cc_start: 0.8334 (mttm) cc_final: 0.8070 (mttm) REVERT: A 451 PHE cc_start: 0.7845 (m-10) cc_final: 0.7564 (m-10) REVERT: A 457 ASN cc_start: 0.8344 (t0) cc_final: 0.7993 (t0) REVERT: H 36 TRP cc_start: 0.7869 (m100) cc_final: 0.7514 (m100) REVERT: H 69 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8207 (p) REVERT: H 71 THR cc_start: 0.8368 (t) cc_final: 0.8123 (p) REVERT: H 90 ASP cc_start: 0.8401 (m-30) cc_final: 0.8106 (t0) REVERT: H 114 GLN cc_start: 0.8422 (pm20) cc_final: 0.7985 (pm20) REVERT: H 152 TYR cc_start: 0.7338 (p90) cc_final: 0.6615 (p90) REVERT: H 188 VAL cc_start: 0.8607 (t) cc_final: 0.8354 (p) REVERT: H 216 LYS cc_start: 0.8782 (tppt) cc_final: 0.8520 (tppp) REVERT: H 217 LYS cc_start: 0.8731 (tttt) cc_final: 0.8454 (tttt) REVERT: L 18 ARG cc_start: 0.7833 (ptm-80) cc_final: 0.7553 (ptm-80) REVERT: L 22 SER cc_start: 0.8426 (p) cc_final: 0.8089 (m) REVERT: L 46 LEU cc_start: 0.7957 (tp) cc_final: 0.7448 (tp) REVERT: L 89 GLN cc_start: 0.8124 (tt0) cc_final: 0.7857 (tt0) REVERT: L 97 MET cc_start: 0.7421 (ttm) cc_final: 0.7162 (ttm) REVERT: L 109 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7988 (tttt) REVERT: L 164 SER cc_start: 0.8556 (t) cc_final: 0.8070 (p) REVERT: L 172 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.7117 (p0) REVERT: L 173 SER cc_start: 0.8797 (OUTLIER) cc_final: 0.8264 (p) REVERT: L 175 TYR cc_start: 0.8182 (m-80) cc_final: 0.7716 (m-80) REVERT: L 201 GLN cc_start: 0.8319 (tt0) cc_final: 0.8062 (tt0) outliers start: 34 outliers final: 23 residues processed: 175 average time/residue: 0.0474 time to fit residues: 11.3986 Evaluate side-chains 184 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 496 VAL 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 96 CYS Chi-restraints excluded: chain H residue 103 ILE 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 109 LYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 0.0770 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.141499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.125337 restraints weight = 7560.435| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.90 r_work: 0.3653 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3641 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 10.314 6782 Z= 0.325 Chirality : 0.045 0.268 750 Planarity : 0.005 0.041 867 Dihedral : 6.535 50.430 699 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 6.47 % Allowed : 21.44 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.89 (0.33), residues: 619 helix: -5.16 (0.24), residues: 12 sheet: -1.24 (0.34), residues: 218 loop : -2.32 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 91 TYR 0.031 0.002 TYR A 442 PHE 0.016 0.002 PHE A 360 TRP 0.030 0.002 TRP H 47 HIS 0.003 0.001 HIS H 171 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 4965) covalent geometry : angle 0.64980 ( 6766) SS BOND : bond 0.00619 ( 8) SS BOND : angle 1.87890 ( 16) hydrogen bonds : bond 0.03132 ( 98) hydrogen bonds : angle 5.46797 ( 240) *********************** 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: 35 poor density : 156 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7326 (m-40) cc_final: 0.7095 (m-40) REVERT: A 342 ARG cc_start: 0.8068 (ptp-110) cc_final: 0.7055 (ptp-110) REVERT: A 379 PHE cc_start: 0.7462 (m-80) cc_final: 0.7142 (m-10) REVERT: A 436 TYR cc_start: 0.8186 (m-80) cc_final: 0.7936 (m-80) REVERT: A 447 LYS cc_start: 0.8288 (mttm) cc_final: 0.8019 (mttm) REVERT: A 451 PHE cc_start: 0.7780 (m-10) cc_final: 0.7562 (m-10) REVERT: A 457 ASN cc_start: 0.8323 (t0) cc_final: 0.7964 (t0) REVERT: H 36 TRP cc_start: 0.7873 (m100) cc_final: 0.7527 (m100) REVERT: H 69 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8214 (p) REVERT: H 71 THR cc_start: 0.8344 (t) cc_final: 0.8093 (p) REVERT: H 90 ASP cc_start: 0.8358 (m-30) cc_final: 0.8063 (t0) REVERT: H 91 THR cc_start: 0.8374 (OUTLIER) cc_final: 0.8116 (p) REVERT: H 114 GLN cc_start: 0.8363 (pm20) cc_final: 0.7944 (pm20) REVERT: H 145 LEU cc_start: 0.8461 (mt) cc_final: 0.8223 (mt) REVERT: H 188 VAL cc_start: 0.8592 (t) cc_final: 0.8303 (p) REVERT: H 216 LYS cc_start: 0.8759 (tppt) cc_final: 0.8498 (tppp) REVERT: H 217 LYS cc_start: 0.8726 (tttt) cc_final: 0.8453 (tttt) REVERT: L 18 ARG cc_start: 0.7853 (ptm-80) cc_final: 0.7581 (ptm-80) REVERT: L 22 SER cc_start: 0.8409 (p) cc_final: 0.8041 (m) REVERT: L 46 LEU cc_start: 0.7910 (tp) cc_final: 0.7546 (tp) REVERT: L 89 GLN cc_start: 0.8098 (tt0) cc_final: 0.7844 (tt0) REVERT: L 164 SER cc_start: 0.8494 (t) cc_final: 0.8010 (p) REVERT: L 172 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7070 (p0) REVERT: L 173 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8251 (p) REVERT: L 175 TYR cc_start: 0.8164 (m-80) cc_final: 0.7748 (m-80) REVERT: L 178 SER cc_start: 0.8462 (t) cc_final: 0.8217 (t) REVERT: L 201 GLN cc_start: 0.8321 (tt0) cc_final: 0.8071 (tt0) outliers start: 35 outliers final: 27 residues processed: 178 average time/residue: 0.0539 time to fit residues: 13.2018 Evaluate side-chains 187 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 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 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 123 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 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 9 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 56 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 0.0970 chunk 34 optimal weight: 0.3980 overall best weight: 0.3378 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.143491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.127926 restraints weight = 7395.849| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.71 r_work: 0.3691 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3650 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= 0.117 Angle : 0.629 11.160 6782 Z= 0.309 Chirality : 0.044 0.260 750 Planarity : 0.005 0.040 867 Dihedral : 6.398 50.112 699 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 6.84 % Allowed : 21.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.34), residues: 619 helix: -5.09 (0.29), residues: 12 sheet: -1.12 (0.34), residues: 226 loop : -2.19 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 91 TYR 0.030 0.001 TYR A 442 PHE 0.009 0.001 PHE A 360 TRP 0.028 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 4965) covalent geometry : angle 0.62319 ( 6766) SS BOND : bond 0.00470 ( 8) SS BOND : angle 1.92360 ( 16) hydrogen bonds : bond 0.02804 ( 98) hydrogen bonds : angle 5.25866 ( 240) *********************** 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 204 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7347 (m-40) cc_final: 0.7139 (m-40) REVERT: A 334 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7216 (m-10) REVERT: A 436 TYR cc_start: 0.8098 (m-80) cc_final: 0.7832 (m-80) REVERT: A 447 LYS cc_start: 0.8154 (mttm) cc_final: 0.7861 (mttm) REVERT: A 457 ASN cc_start: 0.8351 (t0) cc_final: 0.7986 (t0) REVERT: H 36 TRP cc_start: 0.7862 (m100) cc_final: 0.7608 (m100) REVERT: H 69 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8241 (p) REVERT: H 90 ASP cc_start: 0.8197 (m-30) cc_final: 0.7959 (t0) REVERT: H 114 GLN cc_start: 0.8255 (pm20) cc_final: 0.7997 (pm20) REVERT: H 116 THR cc_start: 0.8574 (m) cc_final: 0.8093 (p) REVERT: H 145 LEU cc_start: 0.8465 (mt) cc_final: 0.8203 (mt) REVERT: H 216 LYS cc_start: 0.8683 (tppt) cc_final: 0.8468 (tppp) REVERT: H 217 LYS cc_start: 0.8668 (tttt) cc_final: 0.8433 (tttt) REVERT: L 18 ARG cc_start: 0.7754 (ptm-80) cc_final: 0.7535 (ptm-80) REVERT: L 22 SER cc_start: 0.8366 (p) cc_final: 0.8042 (m) REVERT: L 89 GLN cc_start: 0.8045 (tt0) cc_final: 0.7827 (tt0) REVERT: L 138 LEU cc_start: 0.7517 (mt) cc_final: 0.7315 (mm) REVERT: L 164 SER cc_start: 0.8411 (t) cc_final: 0.7866 (p) REVERT: L 172 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6971 (p0) REVERT: L 173 SER cc_start: 0.8777 (OUTLIER) cc_final: 0.8243 (p) REVERT: L 175 TYR cc_start: 0.8145 (m-80) cc_final: 0.7745 (m-80) REVERT: L 178 SER cc_start: 0.8290 (t) cc_final: 0.7615 (p) REVERT: L 201 GLN cc_start: 0.8180 (tt0) cc_final: 0.7973 (tt0) outliers start: 37 outliers final: 27 residues processed: 187 average time/residue: 0.0452 time to fit residues: 11.9127 Evaluate side-chains 197 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 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 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 26 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 43 optimal weight: 0.0980 chunk 38 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.140340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.124238 restraints weight = 7489.374| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.85 r_work: 0.3634 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 4973 Z= 0.203 Angle : 0.693 12.203 6782 Z= 0.344 Chirality : 0.046 0.286 750 Planarity : 0.005 0.039 867 Dihedral : 6.759 51.952 699 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 6.65 % Allowed : 22.37 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.58 (0.34), residues: 619 helix: -4.89 (0.48), residues: 12 sheet: -1.03 (0.35), residues: 219 loop : -2.10 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 91 TYR 0.034 0.002 TYR A 442 PHE 0.023 0.002 PHE A 451 TRP 0.031 0.002 TRP H 47 HIS 0.004 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 4965) covalent geometry : angle 0.68662 ( 6766) SS BOND : bond 0.00754 ( 8) SS BOND : angle 1.99555 ( 16) hydrogen bonds : bond 0.03369 ( 98) hydrogen bonds : angle 5.34705 ( 240) *********************** 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 205 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7373 (m-40) cc_final: 0.7152 (m-40) REVERT: A 334 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7143 (m-10) REVERT: A 342 ARG cc_start: 0.8091 (ptp-110) cc_final: 0.7049 (ptp-110) REVERT: A 379 PHE cc_start: 0.7502 (m-80) cc_final: 0.7122 (m-10) REVERT: A 383 TYR cc_start: 0.8044 (m-10) cc_final: 0.7386 (m-80) REVERT: A 436 TYR cc_start: 0.8201 (m-80) cc_final: 0.7814 (m-80) REVERT: A 447 LYS cc_start: 0.8294 (mttm) cc_final: 0.8002 (mttm) REVERT: A 457 ASN cc_start: 0.8327 (t0) cc_final: 0.7972 (t0) REVERT: H 36 TRP cc_start: 0.7868 (m100) cc_final: 0.7556 (m100) REVERT: H 69 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8234 (p) REVERT: H 90 ASP cc_start: 0.8353 (m-30) cc_final: 0.8069 (t0) REVERT: H 114 GLN cc_start: 0.8378 (pm20) cc_final: 0.7941 (pm20) REVERT: H 116 THR cc_start: 0.8644 (m) cc_final: 0.8179 (p) REVERT: H 145 LEU cc_start: 0.8460 (mt) cc_final: 0.8147 (mt) REVERT: H 216 LYS cc_start: 0.8753 (tppt) cc_final: 0.8496 (tppp) REVERT: H 217 LYS cc_start: 0.8723 (tttt) cc_final: 0.8466 (tttt) REVERT: L 18 ARG cc_start: 0.7868 (ptm-80) cc_final: 0.7614 (ptm-80) REVERT: L 22 SER cc_start: 0.8410 (p) cc_final: 0.8087 (m) REVERT: L 24 ARG cc_start: 0.7471 (ttm110) cc_final: 0.7085 (ptp-110) REVERT: L 89 GLN cc_start: 0.8142 (tt0) cc_final: 0.7845 (tt0) REVERT: L 164 SER cc_start: 0.8484 (t) cc_final: 0.7958 (p) REVERT: L 172 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.7013 (p0) REVERT: L 173 SER cc_start: 0.8865 (OUTLIER) cc_final: 0.8329 (p) REVERT: L 175 TYR cc_start: 0.8185 (m-80) cc_final: 0.7771 (m-80) REVERT: L 201 GLN cc_start: 0.8292 (tt0) cc_final: 0.7973 (tt0) outliers start: 36 outliers final: 26 residues processed: 188 average time/residue: 0.0501 time to fit residues: 12.6205 Evaluate side-chains 197 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.107 ------------------------------------------------------------------------------- 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 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 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 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 103 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.0570 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.141192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.125340 restraints weight = 7439.094| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.78 r_work: 0.3655 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 4973 Z= 0.153 Angle : 0.674 12.566 6782 Z= 0.332 Chirality : 0.046 0.268 750 Planarity : 0.005 0.041 867 Dihedral : 6.708 51.846 699 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 5.55 % Allowed : 22.92 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.34), residues: 619 helix: -4.64 (0.73), residues: 12 sheet: -1.06 (0.35), residues: 226 loop : -2.04 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 91 TYR 0.032 0.002 TYR A 442 PHE 0.022 0.002 PHE A 451 TRP 0.032 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 4965) covalent geometry : angle 0.66791 ( 6766) SS BOND : bond 0.00767 ( 8) SS BOND : angle 1.94987 ( 16) hydrogen bonds : bond 0.03162 ( 98) hydrogen bonds : angle 5.26718 ( 240) *********************** 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 195 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7395 (m-40) cc_final: 0.7172 (m-40) REVERT: A 334 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7096 (m-10) REVERT: A 342 ARG cc_start: 0.8056 (ptp-110) cc_final: 0.7008 (ptp-110) REVERT: A 383 TYR cc_start: 0.7959 (m-10) cc_final: 0.7293 (m-80) REVERT: A 436 TYR cc_start: 0.8174 (m-80) cc_final: 0.7801 (m-80) REVERT: A 447 LYS cc_start: 0.8256 (mttm) cc_final: 0.7947 (mttm) REVERT: A 457 ASN cc_start: 0.8373 (t0) cc_final: 0.8008 (t0) REVERT: H 36 TRP cc_start: 0.7845 (m100) cc_final: 0.7562 (m100) REVERT: H 69 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8261 (p) REVERT: H 90 ASP cc_start: 0.8295 (m-30) cc_final: 0.8063 (t0) REVERT: H 114 GLN cc_start: 0.8338 (pm20) cc_final: 0.7965 (pm20) REVERT: H 116 THR cc_start: 0.8608 (m) cc_final: 0.8183 (p) REVERT: H 216 LYS cc_start: 0.8728 (tppt) cc_final: 0.8492 (tppp) REVERT: H 217 LYS cc_start: 0.8693 (tttt) cc_final: 0.8441 (tttt) REVERT: L 4 LEU cc_start: 0.8725 (tp) cc_final: 0.8347 (tp) REVERT: L 18 ARG cc_start: 0.7850 (ptm-80) cc_final: 0.7620 (ptm-80) REVERT: L 22 SER cc_start: 0.8406 (p) cc_final: 0.8069 (m) REVERT: L 24 ARG cc_start: 0.7470 (ttm110) cc_final: 0.7054 (ptp-110) REVERT: L 89 GLN cc_start: 0.8135 (tt0) cc_final: 0.7846 (tt0) REVERT: L 97 MET cc_start: 0.6738 (ttm) cc_final: 0.6485 (tmm) REVERT: L 164 SER cc_start: 0.8450 (t) cc_final: 0.7918 (p) REVERT: L 172 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.7010 (p0) REVERT: L 173 SER cc_start: 0.8862 (OUTLIER) cc_final: 0.8329 (p) REVERT: L 175 TYR cc_start: 0.8187 (m-80) cc_final: 0.7821 (m-80) REVERT: L 201 GLN cc_start: 0.8265 (tt0) cc_final: 0.7958 (tt0) outliers start: 30 outliers final: 26 residues processed: 183 average time/residue: 0.0518 time to fit residues: 12.8305 Evaluate side-chains 195 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.101 ------------------------------------------------------------------------------- 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 408 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 496 VAL 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 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 103 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 44 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.141268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.125266 restraints weight = 7481.046| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.87 r_work: 0.3654 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 4973 Z= 0.154 Angle : 0.669 12.326 6782 Z= 0.330 Chirality : 0.045 0.269 750 Planarity : 0.005 0.041 867 Dihedral : 6.741 52.322 699 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.95 % Favored : 88.05 % Rotamer: Outliers : 5.36 % Allowed : 23.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.34), residues: 619 helix: -4.37 (1.00), residues: 12 sheet: -0.94 (0.35), residues: 225 loop : -1.96 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 91 TYR 0.033 0.002 TYR A 442 PHE 0.027 0.002 PHE A 451 TRP 0.033 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4965) covalent geometry : angle 0.66362 ( 6766) SS BOND : bond 0.00765 ( 8) SS BOND : angle 1.92673 ( 16) hydrogen bonds : bond 0.03134 ( 98) hydrogen bonds : angle 5.19965 ( 240) ********************** 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 189 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7403 (m-40) cc_final: 0.7172 (m-40) REVERT: A 334 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.7080 (m-10) REVERT: A 436 TYR cc_start: 0.8198 (m-80) cc_final: 0.7824 (m-80) REVERT: A 447 LYS cc_start: 0.8287 (mttm) cc_final: 0.7967 (mttm) REVERT: A 457 ASN cc_start: 0.8363 (t0) cc_final: 0.7973 (t0) REVERT: H 36 TRP cc_start: 0.7842 (m100) cc_final: 0.7523 (m100) REVERT: H 69 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8227 (p) REVERT: H 90 ASP cc_start: 0.8331 (m-30) cc_final: 0.8090 (t0) REVERT: H 114 GLN cc_start: 0.8341 (pm20) cc_final: 0.7947 (pm20) REVERT: H 116 THR cc_start: 0.8589 (m) cc_final: 0.8163 (p) REVERT: H 216 LYS cc_start: 0.8723 (tppt) cc_final: 0.8463 (tppp) REVERT: H 217 LYS cc_start: 0.8715 (tttt) cc_final: 0.8454 (tttt) REVERT: L 4 LEU cc_start: 0.8704 (tp) cc_final: 0.8222 (tt) REVERT: L 18 ARG cc_start: 0.7854 (ptm-80) cc_final: 0.7610 (ptm-80) REVERT: L 22 SER cc_start: 0.8405 (p) cc_final: 0.8075 (m) REVERT: L 24 ARG cc_start: 0.7503 (ttm110) cc_final: 0.7095 (ptp-110) REVERT: L 89 GLN cc_start: 0.8188 (tt0) cc_final: 0.7864 (tt0) REVERT: L 164 SER cc_start: 0.8484 (t) cc_final: 0.7926 (p) REVERT: L 172 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.7007 (p0) REVERT: L 173 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8346 (p) REVERT: L 175 TYR cc_start: 0.8201 (m-80) cc_final: 0.7839 (m-80) REVERT: L 201 GLN cc_start: 0.8303 (tt0) cc_final: 0.7975 (tt0) outliers start: 29 outliers final: 25 residues processed: 178 average time/residue: 0.0479 time to fit residues: 11.6490 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 : 0.102 ------------------------------------------------------------------------------- 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 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 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 103 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 13 optimal weight: 0.0270 chunk 8 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.140793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.124706 restraints weight = 7510.021| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.87 r_work: 0.3641 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 4973 Z= 0.172 Angle : 0.689 12.132 6782 Z= 0.340 Chirality : 0.046 0.266 750 Planarity : 0.005 0.039 867 Dihedral : 6.830 52.750 699 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 5.73 % Allowed : 23.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.35), residues: 619 helix: -4.34 (1.03), residues: 12 sheet: -0.89 (0.35), residues: 225 loop : -1.91 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 91 TYR 0.033 0.002 TYR A 442 PHE 0.030 0.002 PHE A 451 TRP 0.034 0.002 TRP H 47 HIS 0.004 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 4965) covalent geometry : angle 0.68310 ( 6766) SS BOND : bond 0.00746 ( 8) SS BOND : angle 1.91457 ( 16) hydrogen bonds : bond 0.03279 ( 98) hydrogen bonds : angle 5.26338 ( 240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1224.17 seconds wall clock time: 21 minutes 39.63 seconds (1299.63 seconds total)