Starting phenix.real_space_refine on Tue Feb 11 08:22:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kdt_37145/02_2025/8kdt_37145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kdt_37145/02_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_37145/02_2025/8kdt_37145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kdt_37145/02_2025/8kdt_37145.map" model { file = "/net/cci-nas-00/data/ceres_data/8kdt_37145/02_2025/8kdt_37145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kdt_37145/02_2025/8kdt_37145.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 3075 2.51 5 N 803 2.21 5 O 937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.85, per 1000 atoms: 0.80 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: 1.18 Conformation dependent library (CDL) restraints added in 598.6 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: 0.54 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: 1.17 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: 1.570 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.860 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.600 ------------------------------------------------------------------------------- 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 4965 Z= 0.119 Angle : 0.515 6.049 6766 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 *********************** 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 : 0.483 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: 0.1339 time to fit residues: 35.0096 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 : 0.535 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.146873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.130647 restraints weight = 7424.595| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.91 r_work: 0.3715 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4965 Z= 0.243 Angle : 0.631 6.998 6766 Z= 0.319 Chirality : 0.046 0.184 750 Planarity : 0.005 0.041 867 Dihedral : 6.397 48.454 708 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 6.65 % Allowed : 13.49 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.32), residues: 619 helix: -5.39 (0.31), residues: 6 sheet: -1.90 (0.34), residues: 222 loop : -2.76 (0.30), residues: 391 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 0.014 0.002 PHE A 360 TYR 0.024 0.002 TYR A 442 ARG 0.002 0.000 ARG L 144 *********************** 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: 36 poor density : 161 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 360 PHE cc_start: 0.6351 (OUTLIER) cc_final: 0.5652 (p90) REVERT: A 447 LYS cc_start: 0.8213 (mttm) cc_final: 0.7934 (mttm) REVERT: H 36 TRP cc_start: 0.7853 (m100) cc_final: 0.7563 (m100) REVERT: H 69 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8105 (p) REVERT: H 71 THR cc_start: 0.8424 (t) cc_final: 0.8122 (p) REVERT: H 114 GLN cc_start: 0.8356 (pt0) cc_final: 0.8126 (pm20) REVERT: H 145 LEU cc_start: 0.8358 (mt) cc_final: 0.8013 (mt) REVERT: H 187 SER cc_start: 0.8165 (t) cc_final: 0.7874 (m) REVERT: H 216 LYS cc_start: 0.8706 (tppt) cc_final: 0.8432 (tppp) REVERT: H 217 LYS cc_start: 0.8679 (tttt) cc_final: 0.8389 (tttt) REVERT: L 18 ARG cc_start: 0.7824 (ptm-80) cc_final: 0.7517 (ptm-80) REVERT: L 22 SER cc_start: 0.8373 (p) cc_final: 0.8001 (m) REVERT: L 46 LEU cc_start: 0.7765 (tp) cc_final: 0.7527 (tp) REVERT: L 138 LEU cc_start: 0.7435 (mm) cc_final: 0.7208 (mp) REVERT: L 157 GLN cc_start: 0.7463 (tp40) cc_final: 0.7153 (tp40) REVERT: L 162 GLN cc_start: 0.8494 (mt0) cc_final: 0.8221 (mt0) REVERT: L 164 SER cc_start: 0.8532 (t) cc_final: 0.7913 (p) REVERT: L 172 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7209 (p0) outliers start: 36 outliers final: 22 residues processed: 186 average time/residue: 0.1343 time to fit residues: 33.3020 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 : 0.535 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN L 38 GLN L 160 ASN ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.143316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.127287 restraints weight = 7450.494| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.90 r_work: 0.3677 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4965 Z= 0.270 Angle : 0.642 9.404 6766 Z= 0.324 Chirality : 0.046 0.268 750 Planarity : 0.005 0.041 867 Dihedral : 6.376 49.406 701 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 5.73 % Allowed : 19.22 % Favored : 75.05 % 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: -3.15 (0.33), residues: 619 helix: -5.38 (0.31), residues: 6 sheet: -1.59 (0.35), residues: 216 loop : -2.45 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 47 HIS 0.004 0.001 HIS L 90 PHE 0.015 0.002 PHE A 360 TYR 0.030 0.002 TYR A 442 ARG 0.003 0.000 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7422 (m-40) cc_final: 0.7178 (m-40) REVERT: A 360 PHE cc_start: 0.6423 (OUTLIER) cc_final: 0.5863 (p90) REVERT: A 447 LYS cc_start: 0.8279 (mttm) cc_final: 0.8011 (mttm) REVERT: A 457 ASN cc_start: 0.8340 (t0) cc_final: 0.8082 (t0) REVERT: H 36 TRP cc_start: 0.7867 (m100) cc_final: 0.7507 (m100) REVERT: H 69 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8124 (p) REVERT: H 71 THR cc_start: 0.8385 (t) cc_final: 0.8111 (p) REVERT: H 90 ASP cc_start: 0.8434 (m-30) cc_final: 0.8140 (t0) REVERT: H 114 GLN cc_start: 0.8389 (pt0) cc_final: 0.8151 (pm20) REVERT: H 129 PHE cc_start: 0.7983 (m-10) cc_final: 0.7710 (m-10) REVERT: H 145 LEU cc_start: 0.8398 (mt) cc_final: 0.8129 (mt) REVERT: H 183 TYR cc_start: 0.8188 (m-10) cc_final: 0.7822 (m-10) REVERT: H 187 SER cc_start: 0.8279 (t) cc_final: 0.7935 (m) REVERT: H 188 VAL cc_start: 0.8624 (t) cc_final: 0.8364 (p) REVERT: H 216 LYS cc_start: 0.8742 (tppt) cc_final: 0.8475 (tppp) REVERT: H 217 LYS cc_start: 0.8692 (tttt) cc_final: 0.8398 (tttt) REVERT: L 18 ARG cc_start: 0.7809 (ptm-80) cc_final: 0.7469 (ptm-80) REVERT: L 22 SER cc_start: 0.8402 (p) cc_final: 0.8061 (m) REVERT: L 46 LEU cc_start: 0.7836 (tp) cc_final: 0.7597 (tp) REVERT: L 162 GLN cc_start: 0.8543 (mt0) cc_final: 0.8248 (mt0) REVERT: L 164 SER cc_start: 0.8569 (t) cc_final: 0.7998 (p) REVERT: L 175 TYR cc_start: 0.7981 (m-80) cc_final: 0.7360 (m-80) outliers start: 31 outliers final: 22 residues processed: 178 average time/residue: 0.1303 time to fit residues: 31.1632 Evaluate side-chains 179 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 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: 0.0570 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 0.0060 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN L 27 GLN L 38 GLN L 126 GLN L 191 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.143907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.127879 restraints weight = 7548.146| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.92 r_work: 0.3685 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 4965 Z= 0.201 Angle : 0.612 8.942 6766 Z= 0.304 Chirality : 0.044 0.239 750 Planarity : 0.005 0.039 867 Dihedral : 6.324 48.945 701 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 5.55 % Allowed : 20.52 % 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: -2.96 (0.33), residues: 619 helix: -5.38 (0.30), residues: 6 sheet: -1.44 (0.33), residues: 229 loop : -2.34 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 PHE 0.017 0.002 PHE A 451 TYR 0.029 0.002 TYR A 442 ARG 0.003 0.000 ARG L 91 *********************** 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 188 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7424 (m-40) cc_final: 0.7192 (m-40) REVERT: A 447 LYS cc_start: 0.8267 (mttm) cc_final: 0.7993 (mttm) REVERT: A 457 ASN cc_start: 0.8333 (t0) cc_final: 0.8080 (t0) REVERT: H 36 TRP cc_start: 0.7869 (m100) cc_final: 0.7520 (m100) REVERT: H 69 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8163 (p) REVERT: H 71 THR cc_start: 0.8361 (t) cc_final: 0.8080 (p) REVERT: H 91 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.8037 (p) REVERT: H 114 GLN cc_start: 0.8367 (pt0) cc_final: 0.8112 (pm20) REVERT: H 145 LEU cc_start: 0.8398 (mt) cc_final: 0.8151 (mt) REVERT: H 183 TYR cc_start: 0.8243 (m-10) cc_final: 0.7864 (m-10) REVERT: H 187 SER cc_start: 0.8318 (t) cc_final: 0.7958 (m) REVERT: H 188 VAL cc_start: 0.8619 (t) cc_final: 0.8355 (p) REVERT: H 216 LYS cc_start: 0.8714 (tppt) cc_final: 0.8447 (tppp) REVERT: H 217 LYS cc_start: 0.8647 (tttt) cc_final: 0.8363 (tttt) REVERT: L 18 ARG cc_start: 0.7810 (ptm-80) cc_final: 0.7517 (ptm-80) REVERT: L 22 SER cc_start: 0.8394 (p) cc_final: 0.8054 (m) REVERT: L 46 LEU cc_start: 0.7819 (tp) cc_final: 0.7556 (tp) REVERT: L 164 SER cc_start: 0.8536 (t) cc_final: 0.8080 (p) REVERT: L 172 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7167 (p0) REVERT: L 175 TYR cc_start: 0.8035 (m-80) cc_final: 0.7470 (m-80) outliers start: 30 outliers final: 22 residues processed: 178 average time/residue: 0.1288 time to fit residues: 30.8857 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 : 0.575 ------------------------------------------------------------------------------- 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 117 LEU 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 147 LYS Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 173 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 chunk 53 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.144037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.127936 restraints weight = 7553.237| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.91 r_work: 0.3687 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 4965 Z= 0.189 Angle : 0.618 9.254 6766 Z= 0.305 Chirality : 0.044 0.236 750 Planarity : 0.005 0.038 867 Dihedral : 6.326 49.015 700 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 5.73 % Allowed : 21.44 % Favored : 72.83 % 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: -2.87 (0.33), residues: 619 helix: -5.37 (0.30), residues: 6 sheet: -1.49 (0.32), residues: 238 loop : -2.18 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.014 0.002 PHE H 173 TYR 0.029 0.001 TYR A 442 ARG 0.002 0.000 ARG L 91 *********************** 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 186 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7373 (m-40) cc_final: 0.7140 (m-40) REVERT: A 447 LYS cc_start: 0.8205 (mttm) cc_final: 0.7923 (mttm) REVERT: A 457 ASN cc_start: 0.8332 (t0) cc_final: 0.8062 (t0) REVERT: H 36 TRP cc_start: 0.7854 (m100) cc_final: 0.7525 (m100) REVERT: H 69 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8163 (p) REVERT: H 71 THR cc_start: 0.8356 (t) cc_final: 0.8084 (p) REVERT: H 90 ASP cc_start: 0.8345 (m-30) cc_final: 0.7992 (m-30) REVERT: H 91 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.8033 (p) REVERT: H 114 GLN cc_start: 0.8355 (pt0) cc_final: 0.8123 (pm20) REVERT: H 145 LEU cc_start: 0.8390 (mt) cc_final: 0.8112 (mt) REVERT: H 183 TYR cc_start: 0.8309 (m-10) cc_final: 0.7954 (m-10) REVERT: H 187 SER cc_start: 0.8335 (t) cc_final: 0.7962 (m) REVERT: H 188 VAL cc_start: 0.8595 (t) cc_final: 0.8275 (p) REVERT: H 216 LYS cc_start: 0.8706 (tppt) cc_final: 0.8436 (tppp) REVERT: H 217 LYS cc_start: 0.8653 (tttt) cc_final: 0.8373 (tttt) REVERT: L 18 ARG cc_start: 0.7859 (ptm-80) cc_final: 0.7576 (ptm-80) REVERT: L 22 SER cc_start: 0.8399 (p) cc_final: 0.8050 (m) REVERT: L 46 LEU cc_start: 0.7831 (tp) cc_final: 0.7558 (tp) REVERT: L 164 SER cc_start: 0.8508 (t) cc_final: 0.8027 (p) REVERT: L 172 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7161 (p0) REVERT: L 175 TYR cc_start: 0.8032 (m-80) cc_final: 0.7463 (m-80) REVERT: L 178 SER cc_start: 0.8487 (t) cc_final: 0.8268 (t) outliers start: 31 outliers final: 22 residues processed: 174 average time/residue: 0.1309 time to fit residues: 30.4859 Evaluate side-chains 180 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 CYS 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 117 LEU Chi-restraints excluded: chain H residue 123 THR 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 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: 2.9990 chunk 56 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.0370 chunk 35 optimal weight: 0.0370 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.143734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.128189 restraints weight = 7498.664| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.73 r_work: 0.3703 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 4965 Z= 0.181 Angle : 0.615 10.634 6766 Z= 0.301 Chirality : 0.044 0.272 750 Planarity : 0.005 0.038 867 Dihedral : 6.298 49.290 700 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 5.18 % Allowed : 22.37 % Favored : 72.46 % 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: -2.74 (0.33), residues: 619 helix: -5.02 (0.29), residues: 12 sheet: -1.14 (0.34), residues: 226 loop : -2.23 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 47 HIS 0.002 0.000 HIS L 90 PHE 0.013 0.001 PHE H 173 TYR 0.030 0.001 TYR A 442 ARG 0.002 0.000 ARG L 91 *********************** 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 181 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7412 (m-40) cc_final: 0.7180 (m-40) REVERT: A 447 LYS cc_start: 0.8139 (mttm) cc_final: 0.7863 (mttm) REVERT: A 457 ASN cc_start: 0.8362 (t0) cc_final: 0.8041 (t0) REVERT: H 36 TRP cc_start: 0.7825 (m100) cc_final: 0.7590 (m100) REVERT: H 69 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8234 (p) REVERT: H 71 THR cc_start: 0.8354 (t) cc_final: 0.8103 (p) REVERT: H 90 ASP cc_start: 0.8194 (m-30) cc_final: 0.7854 (m-30) REVERT: H 91 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.8019 (p) REVERT: H 145 LEU cc_start: 0.8458 (mt) cc_final: 0.8177 (mt) REVERT: H 183 TYR cc_start: 0.8355 (m-10) cc_final: 0.8036 (m-10) REVERT: H 187 SER cc_start: 0.8264 (t) cc_final: 0.7966 (m) REVERT: H 216 LYS cc_start: 0.8670 (tppt) cc_final: 0.8441 (tppp) REVERT: H 217 LYS cc_start: 0.8645 (tttt) cc_final: 0.8402 (tttt) REVERT: L 18 ARG cc_start: 0.7749 (ptm-80) cc_final: 0.7523 (ptm-80) REVERT: L 22 SER cc_start: 0.8352 (p) cc_final: 0.8021 (m) REVERT: L 46 LEU cc_start: 0.7794 (tp) cc_final: 0.7525 (tp) REVERT: L 164 SER cc_start: 0.8441 (t) cc_final: 0.8001 (p) REVERT: L 172 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.7125 (p0) REVERT: L 175 TYR cc_start: 0.8078 (m-80) cc_final: 0.7546 (m-80) outliers start: 28 outliers final: 21 residues processed: 170 average time/residue: 0.1258 time to fit residues: 28.9099 Evaluate side-chains 175 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 111 THR Chi-restraints excluded: chain L residue 112 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 52 optimal weight: 0.1980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.143839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.128005 restraints weight = 7336.979| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.83 r_work: 0.3691 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 4965 Z= 0.184 Angle : 0.622 11.744 6766 Z= 0.305 Chirality : 0.044 0.256 750 Planarity : 0.005 0.036 867 Dihedral : 6.394 49.976 700 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 6.10 % Allowed : 22.00 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.33), residues: 619 helix: -4.87 (0.47), residues: 12 sheet: -0.95 (0.35), residues: 216 loop : -2.14 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 47 HIS 0.002 0.000 HIS L 90 PHE 0.027 0.002 PHE A 416 TYR 0.031 0.001 TYR A 442 ARG 0.003 0.000 ARG L 91 *********************** 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 187 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7377 (m-40) cc_final: 0.7145 (m-40) REVERT: A 334 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7015 (m-10) REVERT: A 447 LYS cc_start: 0.8202 (mttm) cc_final: 0.7884 (mttm) REVERT: A 457 ASN cc_start: 0.8378 (t0) cc_final: 0.8051 (t0) REVERT: H 36 TRP cc_start: 0.7838 (m100) cc_final: 0.7531 (m100) REVERT: H 69 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8206 (p) REVERT: H 71 THR cc_start: 0.8329 (t) cc_final: 0.8081 (p) REVERT: H 90 ASP cc_start: 0.8307 (m-30) cc_final: 0.7969 (m-30) REVERT: H 91 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.8053 (p) REVERT: H 145 LEU cc_start: 0.8448 (mt) cc_final: 0.8089 (mt) REVERT: H 183 TYR cc_start: 0.8339 (m-10) cc_final: 0.8048 (m-10) REVERT: H 187 SER cc_start: 0.8308 (t) cc_final: 0.7976 (m) REVERT: H 216 LYS cc_start: 0.8702 (tppt) cc_final: 0.8435 (tppp) REVERT: H 217 LYS cc_start: 0.8704 (tttt) cc_final: 0.8435 (tttt) REVERT: L 18 ARG cc_start: 0.7809 (ptm-80) cc_final: 0.7543 (ptm-80) REVERT: L 22 SER cc_start: 0.8389 (p) cc_final: 0.8027 (m) REVERT: L 138 LEU cc_start: 0.7508 (mt) cc_final: 0.7296 (mm) REVERT: L 164 SER cc_start: 0.8476 (t) cc_final: 0.7968 (p) REVERT: L 172 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7016 (p0) REVERT: L 173 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8215 (p) REVERT: L 175 TYR cc_start: 0.8070 (m-80) cc_final: 0.7578 (m-80) outliers start: 33 outliers final: 24 residues processed: 177 average time/residue: 0.1317 time to fit residues: 31.2656 Evaluate side-chains 183 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 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 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 117 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.0470 chunk 45 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 7 optimal weight: 0.0030 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.5890 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.142186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.126745 restraints weight = 7515.347| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.75 r_work: 0.3676 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 4965 Z= 0.212 Angle : 0.641 12.702 6766 Z= 0.318 Chirality : 0.045 0.260 750 Planarity : 0.005 0.037 867 Dihedral : 6.587 50.744 700 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 6.28 % Allowed : 22.18 % 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 (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: -4.53 (0.81), residues: 12 sheet: -0.84 (0.35), residues: 221 loop : -2.06 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 PHE 0.030 0.002 PHE A 416 TYR 0.032 0.002 TYR A 442 ARG 0.003 0.000 ARG L 91 *********************** 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 187 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7333 (m-40) cc_final: 0.7123 (m-40) REVERT: A 334 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7124 (m-10) REVERT: A 379 PHE cc_start: 0.7454 (m-80) cc_final: 0.7184 (m-10) REVERT: A 447 LYS cc_start: 0.8235 (mttm) cc_final: 0.7937 (mttm) REVERT: A 457 ASN cc_start: 0.8373 (t0) cc_final: 0.7983 (t0) REVERT: H 36 TRP cc_start: 0.7870 (m100) cc_final: 0.7619 (m100) REVERT: H 69 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8254 (p) REVERT: H 71 THR cc_start: 0.8371 (t) cc_final: 0.8122 (p) REVERT: H 90 ASP cc_start: 0.8267 (m-30) cc_final: 0.7931 (m-30) REVERT: H 91 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8078 (p) REVERT: H 145 LEU cc_start: 0.8508 (mt) cc_final: 0.8184 (mt) REVERT: H 183 TYR cc_start: 0.8401 (m-10) cc_final: 0.8076 (m-10) REVERT: H 187 SER cc_start: 0.8243 (t) cc_final: 0.7943 (m) REVERT: H 216 LYS cc_start: 0.8706 (tppt) cc_final: 0.8474 (tppp) REVERT: H 217 LYS cc_start: 0.8683 (tttt) cc_final: 0.8446 (tttt) REVERT: L 18 ARG cc_start: 0.7797 (ptm-80) cc_final: 0.7579 (ptm-80) REVERT: L 22 SER cc_start: 0.8371 (p) cc_final: 0.8034 (m) REVERT: L 138 LEU cc_start: 0.7606 (mt) cc_final: 0.7389 (mm) REVERT: L 164 SER cc_start: 0.8442 (t) cc_final: 0.7952 (p) REVERT: L 172 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.6993 (p0) REVERT: L 173 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8234 (p) REVERT: L 175 TYR cc_start: 0.8141 (m-80) cc_final: 0.7724 (m-80) outliers start: 34 outliers final: 26 residues processed: 175 average time/residue: 0.1355 time to fit residues: 31.8099 Evaluate side-chains 184 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 49 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 30 optimal weight: 0.0050 chunk 53 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.141136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.125888 restraints weight = 7445.857| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.70 r_work: 0.3666 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 4965 Z= 0.240 Angle : 0.669 12.194 6766 Z= 0.335 Chirality : 0.046 0.263 750 Planarity : 0.005 0.037 867 Dihedral : 6.842 53.700 700 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 6.28 % Allowed : 22.18 % 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 (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: -2.40 (0.34), residues: 619 helix: -4.32 (1.05), residues: 12 sheet: -0.85 (0.35), residues: 221 loop : -2.04 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 161 HIS 0.003 0.001 HIS L 90 PHE 0.030 0.002 PHE A 416 TYR 0.032 0.002 TYR A 442 ARG 0.004 0.000 ARG L 91 *********************** 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 186 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7371 (m-40) cc_final: 0.7153 (m-40) REVERT: A 334 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7089 (m-10) REVERT: A 447 LYS cc_start: 0.8236 (mttm) cc_final: 0.7943 (mttm) REVERT: A 457 ASN cc_start: 0.8376 (t0) cc_final: 0.8004 (t0) REVERT: H 36 TRP cc_start: 0.7873 (m100) cc_final: 0.7623 (m100) REVERT: H 69 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8245 (p) REVERT: H 71 THR cc_start: 0.8369 (t) cc_final: 0.8134 (p) REVERT: H 90 ASP cc_start: 0.8258 (m-30) cc_final: 0.7928 (m-30) REVERT: H 91 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8102 (p) REVERT: H 111 TYR cc_start: 0.7902 (m-80) cc_final: 0.7654 (m-80) REVERT: H 114 GLN cc_start: 0.8317 (pm20) cc_final: 0.8102 (pm20) REVERT: H 145 LEU cc_start: 0.8503 (mt) cc_final: 0.8168 (mt) REVERT: H 183 TYR cc_start: 0.8417 (m-10) cc_final: 0.8091 (m-10) REVERT: H 187 SER cc_start: 0.8261 (t) cc_final: 0.7952 (m) REVERT: H 216 LYS cc_start: 0.8708 (tppt) cc_final: 0.8478 (tppp) REVERT: H 217 LYS cc_start: 0.8672 (tttt) cc_final: 0.8430 (tttt) REVERT: L 18 ARG cc_start: 0.7758 (ptm-80) cc_final: 0.7549 (ptm-80) REVERT: L 22 SER cc_start: 0.8379 (p) cc_final: 0.8057 (m) REVERT: L 89 GLN cc_start: 0.8114 (tt0) cc_final: 0.7847 (tt0) REVERT: L 164 SER cc_start: 0.8456 (t) cc_final: 0.7929 (p) REVERT: L 172 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.7030 (p0) REVERT: L 173 SER cc_start: 0.8813 (OUTLIER) cc_final: 0.8278 (p) REVERT: L 175 TYR cc_start: 0.8189 (m-80) cc_final: 0.7831 (m-80) REVERT: L 201 GLN cc_start: 0.8137 (tt0) cc_final: 0.7870 (tt0) REVERT: L 209 LYS cc_start: 0.7336 (mmtt) cc_final: 0.7129 (mmtt) outliers start: 34 outliers final: 25 residues processed: 172 average time/residue: 0.1305 time to fit residues: 30.0748 Evaluate side-chains 182 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 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 99 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: 0.9990 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.139972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.124233 restraints weight = 7574.325| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.85 r_work: 0.3634 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 4965 Z= 0.274 Angle : 0.718 13.216 6766 Z= 0.357 Chirality : 0.047 0.273 750 Planarity : 0.005 0.036 867 Dihedral : 7.010 52.371 700 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 5.36 % Allowed : 24.21 % Favored : 70.43 % 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: -2.34 (0.34), residues: 619 helix: -4.31 (1.07), residues: 12 sheet: -0.89 (0.35), residues: 223 loop : -1.95 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 47 HIS 0.004 0.001 HIS L 90 PHE 0.035 0.002 PHE A 416 TYR 0.033 0.002 TYR A 442 ARG 0.004 0.000 ARG L 91 ********************** 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 185 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7404 (m-40) cc_final: 0.7172 (m-40) REVERT: A 334 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7065 (m-10) REVERT: A 447 LYS cc_start: 0.8274 (mttm) cc_final: 0.7968 (mttm) REVERT: A 457 ASN cc_start: 0.8388 (t0) cc_final: 0.8021 (t0) REVERT: H 36 TRP cc_start: 0.7867 (m100) cc_final: 0.7578 (m100) REVERT: H 69 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.8235 (p) REVERT: H 71 THR cc_start: 0.8370 (t) cc_final: 0.8125 (p) REVERT: H 90 ASP cc_start: 0.8362 (m-30) cc_final: 0.8036 (t0) REVERT: H 114 GLN cc_start: 0.8390 (pm20) cc_final: 0.8061 (pm20) REVERT: H 145 LEU cc_start: 0.8481 (mt) cc_final: 0.8142 (mt) REVERT: H 187 SER cc_start: 0.8322 (t) cc_final: 0.7988 (m) REVERT: H 216 LYS cc_start: 0.8718 (tppt) cc_final: 0.8460 (tppp) REVERT: H 217 LYS cc_start: 0.8715 (tttt) cc_final: 0.8458 (tttt) REVERT: L 18 ARG cc_start: 0.7849 (ptm-80) cc_final: 0.7598 (ptm-80) REVERT: L 22 SER cc_start: 0.8406 (p) cc_final: 0.8073 (m) REVERT: L 89 GLN cc_start: 0.8174 (tt0) cc_final: 0.7823 (tt0) REVERT: L 164 SER cc_start: 0.8475 (t) cc_final: 0.7899 (p) REVERT: L 172 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.7045 (p0) REVERT: L 173 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8319 (p) REVERT: L 175 TYR cc_start: 0.8239 (m-80) cc_final: 0.7833 (m-80) REVERT: L 201 GLN cc_start: 0.8234 (tt0) cc_final: 0.7910 (tt0) outliers start: 29 outliers final: 23 residues processed: 174 average time/residue: 0.1368 time to fit residues: 31.9682 Evaluate side-chains 179 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 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 91 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 196 LEU 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 112 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3955 r_free = 0.3955 target = 0.140085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.124265 restraints weight = 7496.701| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.84 r_work: 0.3636 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 4965 Z= 0.275 Angle : 0.740 18.740 6766 Z= 0.365 Chirality : 0.046 0.266 750 Planarity : 0.005 0.038 867 Dihedral : 7.069 58.062 700 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 5.36 % Allowed : 25.32 % Favored : 69.32 % 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: -2.30 (0.34), residues: 619 helix: -4.13 (1.24), residues: 12 sheet: -0.86 (0.35), residues: 224 loop : -1.93 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 PHE 0.032 0.003 PHE A 416 TYR 0.033 0.002 TYR A 442 ARG 0.004 0.000 ARG L 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2787.28 seconds wall clock time: 50 minutes 19.53 seconds (3019.53 seconds total)