Starting phenix.real_space_refine on Sat Apr 26 22:21:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sib_40505/04_2025/8sib_40505.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sib_40505/04_2025/8sib_40505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sib_40505/04_2025/8sib_40505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sib_40505/04_2025/8sib_40505.map" model { file = "/net/cci-nas-00/data/ceres_data/8sib_40505/04_2025/8sib_40505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sib_40505/04_2025/8sib_40505.cif" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 18 5.16 5 C 2261 2.51 5 N 619 2.21 5 O 646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3544 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3544 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 436} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 4.52, per 1000 atoms: 1.28 Number of scatterers: 3544 At special positions: 0 Unit cell: (66.4, 94.62, 74.7, 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 18 16.00 O 646 8.00 N 619 7.00 C 2261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 44 " distance=2.04 Simple disulfide: pdb=" SG CYS A 33 " - pdb=" SG CYS A 36 " distance=2.04 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 44 " distance=2.04 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: 0.99 Conformation dependent library (CDL) restraints added in 495.8 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 840 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 38.5% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 116 through 125 removed outlier: 3.534A pdb=" N LEU A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 167 removed outlier: 3.511A pdb=" N LEU A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 191 removed outlier: 4.447A pdb=" N HIS A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 258 through 273 removed outlier: 4.302A pdb=" N LEU A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.755A pdb=" N GLN A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 331 removed outlier: 3.624A pdb=" N GLN A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.832A pdb=" N THR A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 372 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 390 through 398 removed outlier: 3.538A pdb=" N ALA A 394 " --> pdb=" O ASP A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 418 Processing helix chain 'A' and resid 419 through 426 removed outlier: 3.943A pdb=" N ALA A 423 " --> pdb=" O ARG A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 449 removed outlier: 3.507A pdb=" N LEU A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.823A pdb=" N GLU A 15 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 94 removed outlier: 6.479A pdb=" N LYS A 107 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU A 247 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL A 109 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ASP A 249 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU A 111 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR A 201 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE A 246 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY A 203 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 248 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA A 205 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N CYS A 200 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A 135 " --> pdb=" O TRP A 170 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU A 172 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 137 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 312 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N PHE A 381 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 314 " --> pdb=" O PHE A 381 " (cutoff:3.500A) 117 hydrogen bonds defined for protein. 342 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: 0.87 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1156 1.34 - 1.47: 780 1.47 - 1.59: 1652 1.59 - 1.71: 0 1.71 - 1.83: 26 Bond restraints: 3614 Sorted by residual: bond pdb=" C GLU A 343 " pdb=" N PRO A 344 " ideal model delta sigma weight residual 1.336 1.370 -0.034 1.25e-02 6.40e+03 7.38e+00 bond pdb=" N SER A 101 " pdb=" CA SER A 101 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.16e+00 bond pdb=" C LEU A 30 " pdb=" N PRO A 31 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.04e+00 bond pdb=" C SER A 307 " pdb=" N PRO A 308 " ideal model delta sigma weight residual 1.329 1.353 -0.024 1.18e-02 7.18e+03 4.02e+00 bond pdb=" CB ILE A 412 " pdb=" CG2 ILE A 412 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.36e+00 ... (remaining 3609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 4661 2.66 - 5.32: 200 5.32 - 7.98: 21 7.98 - 10.64: 10 10.64 - 13.30: 4 Bond angle restraints: 4896 Sorted by residual: angle pdb=" C ARG A 46 " pdb=" N LEU A 47 " pdb=" CA LEU A 47 " ideal model delta sigma weight residual 121.54 133.47 -11.93 1.91e+00 2.74e-01 3.90e+01 angle pdb=" C GLU A 76 " pdb=" N GLU A 77 " pdb=" CA GLU A 77 " ideal model delta sigma weight residual 122.46 129.98 -7.52 1.41e+00 5.03e-01 2.84e+01 angle pdb=" C CYS A 36 " pdb=" N GLN A 37 " pdb=" CA GLN A 37 " ideal model delta sigma weight residual 121.54 131.32 -9.78 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C VAL A 48 " pdb=" N LYS A 49 " pdb=" CA LYS A 49 " ideal model delta sigma weight residual 121.54 130.64 -9.10 1.91e+00 2.74e-01 2.27e+01 angle pdb=" C GLY A 100 " pdb=" N SER A 101 " pdb=" CA SER A 101 " ideal model delta sigma weight residual 121.54 130.39 -8.85 1.91e+00 2.74e-01 2.15e+01 ... (remaining 4891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.41: 2018 15.41 - 30.83: 117 30.83 - 46.24: 29 46.24 - 61.66: 8 61.66 - 77.07: 7 Dihedral angle restraints: 2179 sinusoidal: 877 harmonic: 1302 Sorted by residual: dihedral pdb=" CA SER A 307 " pdb=" C SER A 307 " pdb=" N PRO A 308 " pdb=" CA PRO A 308 " ideal model delta harmonic sigma weight residual -180.00 -123.29 -56.71 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA LEU A 30 " pdb=" C LEU A 30 " pdb=" N PRO A 31 " pdb=" CA PRO A 31 " ideal model delta harmonic sigma weight residual -180.00 -126.99 -53.01 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA ILE A 383 " pdb=" C ILE A 383 " pdb=" N GLY A 384 " pdb=" CA GLY A 384 " ideal model delta harmonic sigma weight residual -180.00 -131.62 -48.38 0 5.00e+00 4.00e-02 9.36e+01 ... (remaining 2176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 438 0.065 - 0.130: 103 0.130 - 0.195: 19 0.195 - 0.260: 1 0.260 - 0.325: 5 Chirality restraints: 566 Sorted by residual: chirality pdb=" CB VAL A 176 " pdb=" CA VAL A 176 " pdb=" CG1 VAL A 176 " pdb=" CG2 VAL A 176 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CG LEU A 47 " pdb=" CB LEU A 47 " pdb=" CD1 LEU A 47 " pdb=" CD2 LEU A 47 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE A 383 " pdb=" CA ILE A 383 " pdb=" CG1 ILE A 383 " pdb=" CG2 ILE A 383 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 563 not shown) Planarity restraints: 622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 95 " 0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ILE A 95 " -0.062 2.00e-02 2.50e+03 pdb=" O ILE A 95 " 0.023 2.00e-02 2.50e+03 pdb=" N ASN A 96 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 30 " -0.058 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO A 31 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 31 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C PRO A 31 " 0.055 2.00e-02 2.50e+03 pdb=" O PRO A 31 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY A 32 " -0.018 2.00e-02 2.50e+03 ... (remaining 619 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 836 2.79 - 3.32: 3127 3.32 - 3.85: 5541 3.85 - 4.37: 6449 4.37 - 4.90: 11243 Nonbonded interactions: 27196 Sorted by model distance: nonbonded pdb=" O PHE A 290 " pdb=" OG1 THR A 318 " model vdw 2.265 3.040 nonbonded pdb=" O ALA A 163 " pdb=" OG1 THR A 167 " model vdw 2.324 3.040 nonbonded pdb=" OH TYR A 108 " pdb=" O LEU A 216 " model vdw 2.338 3.040 nonbonded pdb=" NH1 ARG A 41 " pdb=" O ARG A 46 " model vdw 2.348 3.120 nonbonded pdb=" N LEU A 30 " pdb=" O LEU A 30 " model vdw 2.374 2.496 ... (remaining 27191 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 17.470 Find NCS groups from input model: 0.030 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:13.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 : 0.007 0.060 3617 Z= 0.320 Angle : 1.312 13.305 4902 Z= 0.756 Chirality : 0.064 0.325 566 Planarity : 0.008 0.088 622 Dihedral : 11.699 75.711 1330 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 1.33 % Allowed : 12.89 % Favored : 85.78 % Rotamer: Outliers : 0.78 % Allowed : 3.88 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 17.65 % Twisted General : 0.92 % 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: -5.28 (0.28), residues: 450 helix: -4.12 (0.18), residues: 167 sheet: -1.75 (0.55), residues: 62 loop : -3.55 (0.33), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 6 HIS 0.012 0.002 HIS A 242 PHE 0.021 0.004 PHE A 381 TYR 0.028 0.003 TYR A 108 ARG 0.007 0.001 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.31640 ( 117) hydrogen bonds : angle 9.31291 ( 342) SS BOND : bond 0.00735 ( 3) SS BOND : angle 4.21702 ( 6) covalent geometry : bond 0.00669 ( 3614) covalent geometry : angle 1.30401 ( 4896) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 102 HIS cc_start: 0.7321 (m-70) cc_final: 0.6998 (m170) REVERT: A 198 LYS cc_start: 0.8504 (mmtt) cc_final: 0.7943 (ttpp) REVERT: A 211 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7185 (mm-30) REVERT: A 352 LYS cc_start: 0.9076 (mtmm) cc_final: 0.8615 (mttp) REVERT: A 370 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8435 (mm-30) outliers start: 3 outliers final: 1 residues processed: 80 average time/residue: 1.3253 time to fit residues: 108.9387 Evaluate side-chains 43 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 22 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 86 GLN A 144 GLN A 154 GLN A 276 HIS A 404 ASN A 432 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.128148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097883 restraints weight = 6436.332| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.80 r_work: 0.3328 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3617 Z= 0.172 Angle : 0.843 11.468 4902 Z= 0.428 Chirality : 0.047 0.247 566 Planarity : 0.006 0.075 622 Dihedral : 7.546 41.602 483 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.89 % Allowed : 13.11 % Favored : 86.00 % Rotamer: Outliers : 3.36 % Allowed : 11.63 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.69 % 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: -3.55 (0.33), residues: 450 helix: -1.49 (0.34), residues: 178 sheet: -2.09 (0.60), residues: 51 loop : -3.23 (0.35), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 78 HIS 0.006 0.001 HIS A 51 PHE 0.010 0.001 PHE A 146 TYR 0.009 0.001 TYR A 327 ARG 0.007 0.001 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 117) hydrogen bonds : angle 4.78675 ( 342) SS BOND : bond 0.00908 ( 3) SS BOND : angle 3.73972 ( 6) covalent geometry : bond 0.00386 ( 3614) covalent geometry : angle 0.83281 ( 4896) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 37 GLN cc_start: 0.6745 (OUTLIER) cc_final: 0.6471 (mm-40) REVERT: A 85 GLU cc_start: 0.7137 (tp30) cc_final: 0.6513 (tt0) REVERT: A 102 HIS cc_start: 0.7173 (m-70) cc_final: 0.6786 (t-90) REVERT: A 131 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8059 (mm-30) REVERT: A 198 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8276 (tttt) REVERT: A 340 ASP cc_start: 0.8790 (t70) cc_final: 0.8482 (p0) REVERT: A 349 THR cc_start: 0.8781 (m) cc_final: 0.8481 (t) REVERT: A 352 LYS cc_start: 0.9223 (mtmm) cc_final: 0.8742 (mppt) REVERT: A 370 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8530 (mm-30) REVERT: A 460 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8242 (tm-30) outliers start: 13 outliers final: 1 residues processed: 61 average time/residue: 1.2417 time to fit residues: 78.1615 Evaluate side-chains 43 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.126081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.095941 restraints weight = 6316.742| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.71 r_work: 0.3269 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3617 Z= 0.185 Angle : 0.859 14.851 4902 Z= 0.422 Chirality : 0.046 0.178 566 Planarity : 0.004 0.042 622 Dihedral : 7.140 44.768 481 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.67 % Allowed : 13.33 % Favored : 86.00 % Rotamer: Outliers : 2.84 % Allowed : 12.40 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % Twisted General : 0.46 % 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: -2.64 (0.37), residues: 450 helix: -0.21 (0.38), residues: 178 sheet: -2.01 (0.59), residues: 51 loop : -3.11 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 207 HIS 0.006 0.001 HIS A 51 PHE 0.008 0.001 PHE A 356 TYR 0.009 0.001 TYR A 327 ARG 0.006 0.001 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 117) hydrogen bonds : angle 4.15454 ( 342) SS BOND : bond 0.01368 ( 3) SS BOND : angle 4.51375 ( 6) covalent geometry : bond 0.00421 ( 3614) covalent geometry : angle 0.84522 ( 4896) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7179 (tp30) cc_final: 0.6568 (tt0) REVERT: A 102 HIS cc_start: 0.7259 (m-70) cc_final: 0.6857 (t-90) REVERT: A 131 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8079 (mm-30) REVERT: A 198 LYS cc_start: 0.8786 (mmtt) cc_final: 0.8268 (tttt) REVERT: A 211 GLU cc_start: 0.8516 (tp30) cc_final: 0.8093 (mm-30) REVERT: A 291 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: A 340 ASP cc_start: 0.8853 (t70) cc_final: 0.8595 (p0) REVERT: A 460 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8216 (tm-30) outliers start: 11 outliers final: 3 residues processed: 50 average time/residue: 1.2872 time to fit residues: 66.4790 Evaluate side-chains 40 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 303 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.125504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.095171 restraints weight = 6363.642| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.71 r_work: 0.3295 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3617 Z= 0.194 Angle : 0.837 16.217 4902 Z= 0.415 Chirality : 0.048 0.255 566 Planarity : 0.004 0.042 622 Dihedral : 6.934 40.145 481 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.89 % Allowed : 12.89 % Favored : 86.22 % Rotamer: Outliers : 4.39 % Allowed : 13.18 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % Twisted General : 0.46 % 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: -2.26 (0.38), residues: 450 helix: 0.27 (0.40), residues: 177 sheet: -1.95 (0.61), residues: 51 loop : -2.99 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 207 HIS 0.006 0.001 HIS A 51 PHE 0.020 0.002 PHE A 354 TYR 0.005 0.001 TYR A 327 ARG 0.004 0.001 ARG A 46 Details of bonding type rmsd hydrogen bonds : bond 0.03278 ( 117) hydrogen bonds : angle 4.07098 ( 342) SS BOND : bond 0.01470 ( 3) SS BOND : angle 4.57465 ( 6) covalent geometry : bond 0.00449 ( 3614) covalent geometry : angle 0.82227 ( 4896) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7184 (tp30) cc_final: 0.6614 (tt0) REVERT: A 92 TYR cc_start: 0.8825 (p90) cc_final: 0.7732 (p90) REVERT: A 102 HIS cc_start: 0.7237 (m-70) cc_final: 0.6838 (t-90) REVERT: A 131 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8153 (mm-30) REVERT: A 198 LYS cc_start: 0.8807 (mmtt) cc_final: 0.8288 (tttt) REVERT: A 340 ASP cc_start: 0.8868 (t70) cc_final: 0.8627 (p0) REVERT: A 460 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8292 (tm-30) outliers start: 17 outliers final: 6 residues processed: 58 average time/residue: 1.0881 time to fit residues: 65.4615 Evaluate side-chains 45 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 71 PHE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 371 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 44 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.0170 chunk 0 optimal weight: 0.5980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.123773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.094328 restraints weight = 6254.178| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.54 r_work: 0.3258 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3617 Z= 0.143 Angle : 0.813 16.960 4902 Z= 0.395 Chirality : 0.047 0.225 566 Planarity : 0.005 0.079 622 Dihedral : 6.659 38.849 481 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.67 % Allowed : 13.33 % Favored : 86.00 % Rotamer: Outliers : 4.13 % Allowed : 17.57 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 11.76 % Twisted General : 0.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.40), residues: 450 helix: 0.60 (0.41), residues: 178 sheet: -1.59 (0.63), residues: 49 loop : -2.83 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 207 HIS 0.004 0.001 HIS A 51 PHE 0.017 0.001 PHE A 356 TYR 0.010 0.001 TYR A 327 ARG 0.003 0.000 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.02788 ( 117) hydrogen bonds : angle 3.89731 ( 342) SS BOND : bond 0.01470 ( 3) SS BOND : angle 4.50112 ( 6) covalent geometry : bond 0.00322 ( 3614) covalent geometry : angle 0.79769 ( 4896) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.423 Fit side-chains REVERT: A 85 GLU cc_start: 0.7278 (tp30) cc_final: 0.6809 (tt0) REVERT: A 102 HIS cc_start: 0.7327 (m-70) cc_final: 0.6995 (t-90) REVERT: A 198 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8288 (tttt) REVERT: A 211 GLU cc_start: 0.8511 (tp30) cc_final: 0.7991 (mm-30) REVERT: A 291 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7035 (tt0) REVERT: A 302 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7336 (pp20) REVERT: A 352 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8608 (mtmt) REVERT: A 358 GLN cc_start: 0.8826 (mm110) cc_final: 0.8378 (tp40) REVERT: A 460 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8350 (tm-30) outliers start: 16 outliers final: 5 residues processed: 53 average time/residue: 1.0545 time to fit residues: 58.0298 Evaluate side-chains 44 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 371 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 0.0970 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.0050 chunk 33 optimal weight: 0.0980 chunk 41 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 0.0050 chunk 37 optimal weight: 0.9990 overall best weight: 0.1606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 50 GLN A 154 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.134094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.105818 restraints weight = 6708.657| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 3.80 r_work: 0.3439 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3617 Z= 0.123 Angle : 0.783 17.597 4902 Z= 0.382 Chirality : 0.046 0.205 566 Planarity : 0.004 0.062 622 Dihedral : 6.234 36.419 481 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.44 % Allowed : 12.22 % Favored : 87.33 % Rotamer: Outliers : 3.10 % Allowed : 18.09 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.40), residues: 450 helix: 0.95 (0.42), residues: 178 sheet: -1.19 (0.66), residues: 49 loop : -2.72 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 6 HIS 0.004 0.001 HIS A 51 PHE 0.012 0.001 PHE A 356 TYR 0.008 0.001 TYR A 92 ARG 0.004 0.000 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.02383 ( 117) hydrogen bonds : angle 3.71961 ( 342) SS BOND : bond 0.01496 ( 3) SS BOND : angle 4.42209 ( 6) covalent geometry : bond 0.00259 ( 3614) covalent geometry : angle 0.76834 ( 4896) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 102 HIS cc_start: 0.7289 (m-70) cc_final: 0.7017 (t-90) REVERT: A 151 ARG cc_start: 0.8667 (tpt170) cc_final: 0.8458 (tpm170) REVERT: A 198 LYS cc_start: 0.8706 (mmtt) cc_final: 0.8194 (tttt) REVERT: A 211 GLU cc_start: 0.8570 (tp30) cc_final: 0.8077 (mm-30) REVERT: A 291 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: A 327 TYR cc_start: 0.8782 (t80) cc_final: 0.8581 (t80) REVERT: A 358 GLN cc_start: 0.8810 (mm110) cc_final: 0.8316 (tp40) REVERT: A 435 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8450 (pp) REVERT: A 460 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8301 (tm-30) outliers start: 12 outliers final: 5 residues processed: 55 average time/residue: 1.1496 time to fit residues: 65.4714 Evaluate side-chains 42 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 435 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 43 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 HIS A 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.130092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.101641 restraints weight = 6688.248| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.76 r_work: 0.3388 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3617 Z= 0.171 Angle : 0.824 16.910 4902 Z= 0.403 Chirality : 0.048 0.259 566 Planarity : 0.005 0.051 622 Dihedral : 6.162 34.555 481 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.67 % Allowed : 13.11 % Favored : 86.22 % Rotamer: Outliers : 3.36 % Allowed : 19.64 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.69 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.40), residues: 450 helix: 0.82 (0.41), residues: 179 sheet: -1.26 (0.66), residues: 49 loop : -2.72 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 207 HIS 0.006 0.001 HIS A 51 PHE 0.013 0.002 PHE A 356 TYR 0.008 0.001 TYR A 108 ARG 0.004 0.000 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.03054 ( 117) hydrogen bonds : angle 3.85358 ( 342) SS BOND : bond 0.01257 ( 3) SS BOND : angle 4.33463 ( 6) covalent geometry : bond 0.00399 ( 3614) covalent geometry : angle 0.81082 ( 4896) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.401 Fit side-chains REVERT: A 85 GLU cc_start: 0.7167 (tp30) cc_final: 0.6624 (tt0) REVERT: A 92 TYR cc_start: 0.8834 (p90) cc_final: 0.8059 (p90) REVERT: A 102 HIS cc_start: 0.7313 (m-70) cc_final: 0.6958 (t-90) REVERT: A 114 ASP cc_start: 0.8716 (t70) cc_final: 0.8399 (t0) REVERT: A 151 ARG cc_start: 0.8735 (tpt170) cc_final: 0.8366 (tpm170) REVERT: A 198 LYS cc_start: 0.8755 (mmtt) cc_final: 0.8271 (tttt) REVERT: A 211 GLU cc_start: 0.8537 (tp30) cc_final: 0.8023 (mm-30) REVERT: A 291 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: A 358 GLN cc_start: 0.8935 (mm110) cc_final: 0.8397 (tp40) REVERT: A 435 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8491 (pp) REVERT: A 460 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8325 (tm-30) outliers start: 13 outliers final: 6 residues processed: 49 average time/residue: 1.0545 time to fit residues: 53.7874 Evaluate side-chains 45 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 194 ARG Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 435 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 5 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.129716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.101266 restraints weight = 6670.498| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.72 r_work: 0.3383 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3617 Z= 0.173 Angle : 0.812 13.722 4902 Z= 0.401 Chirality : 0.048 0.239 566 Planarity : 0.004 0.041 622 Dihedral : 6.084 33.084 481 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.67 % Allowed : 13.11 % Favored : 86.22 % Rotamer: Outliers : 2.84 % Allowed : 20.67 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.40), residues: 450 helix: 0.79 (0.41), residues: 179 sheet: -1.29 (0.67), residues: 49 loop : -2.75 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 207 HIS 0.006 0.001 HIS A 51 PHE 0.013 0.001 PHE A 356 TYR 0.008 0.001 TYR A 108 ARG 0.003 0.000 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 117) hydrogen bonds : angle 3.94961 ( 342) SS BOND : bond 0.01133 ( 3) SS BOND : angle 4.22052 ( 6) covalent geometry : bond 0.00405 ( 3614) covalent geometry : angle 0.79878 ( 4896) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.441 Fit side-chains REVERT: A 85 GLU cc_start: 0.7161 (tp30) cc_final: 0.6622 (tt0) REVERT: A 92 TYR cc_start: 0.8763 (p90) cc_final: 0.7968 (p90) REVERT: A 102 HIS cc_start: 0.7336 (m-70) cc_final: 0.6972 (t-90) REVERT: A 114 ASP cc_start: 0.8755 (t70) cc_final: 0.8442 (t0) REVERT: A 198 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8255 (tttt) REVERT: A 211 GLU cc_start: 0.8531 (tp30) cc_final: 0.8000 (mm-30) REVERT: A 302 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7269 (pp20) REVERT: A 358 GLN cc_start: 0.8948 (mm110) cc_final: 0.8393 (tp40) REVERT: A 435 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8488 (pp) REVERT: A 460 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8335 (tm-30) outliers start: 11 outliers final: 5 residues processed: 47 average time/residue: 1.3071 time to fit residues: 63.5157 Evaluate side-chains 44 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 435 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 4 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.130828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.102629 restraints weight = 6523.601| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.68 r_work: 0.3401 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3617 Z= 0.153 Angle : 0.811 15.856 4902 Z= 0.398 Chirality : 0.048 0.232 566 Planarity : 0.004 0.042 622 Dihedral : 6.045 34.110 481 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.56 % Favored : 86.00 % Rotamer: Outliers : 2.84 % Allowed : 21.19 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.40), residues: 450 helix: 0.86 (0.41), residues: 179 sheet: -1.26 (0.67), residues: 49 loop : -2.71 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 207 HIS 0.006 0.001 HIS A 51 PHE 0.012 0.001 PHE A 356 TYR 0.012 0.001 TYR A 327 ARG 0.006 0.001 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.02868 ( 117) hydrogen bonds : angle 3.95437 ( 342) SS BOND : bond 0.01191 ( 3) SS BOND : angle 4.26365 ( 6) covalent geometry : bond 0.00351 ( 3614) covalent geometry : angle 0.79767 ( 4896) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.388 Fit side-chains REVERT: A 85 GLU cc_start: 0.7143 (tp30) cc_final: 0.6619 (tt0) REVERT: A 92 TYR cc_start: 0.8818 (p90) cc_final: 0.7919 (p90) REVERT: A 102 HIS cc_start: 0.7357 (m-70) cc_final: 0.6979 (t-90) REVERT: A 114 ASP cc_start: 0.8707 (t70) cc_final: 0.8420 (t0) REVERT: A 198 LYS cc_start: 0.8705 (mmtt) cc_final: 0.8242 (tttt) REVERT: A 211 GLU cc_start: 0.8531 (tp30) cc_final: 0.8035 (mm-30) REVERT: A 302 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7215 (pp20) REVERT: A 358 GLN cc_start: 0.8947 (mm110) cc_final: 0.8397 (tp40) REVERT: A 435 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8403 (pp) REVERT: A 460 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8337 (tm-30) outliers start: 11 outliers final: 5 residues processed: 51 average time/residue: 1.0902 time to fit residues: 57.8529 Evaluate side-chains 45 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 435 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.129806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.101413 restraints weight = 6685.826| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.70 r_work: 0.3307 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3617 Z= 0.171 Angle : 0.819 16.414 4902 Z= 0.403 Chirality : 0.048 0.219 566 Planarity : 0.004 0.043 622 Dihedral : 6.151 34.993 481 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.67 % Allowed : 13.56 % Favored : 85.78 % Rotamer: Outliers : 1.81 % Allowed : 23.00 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.40), residues: 450 helix: 0.78 (0.41), residues: 179 sheet: -1.32 (0.66), residues: 49 loop : -2.75 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 207 HIS 0.006 0.001 HIS A 51 PHE 0.012 0.001 PHE A 356 TYR 0.008 0.001 TYR A 108 ARG 0.006 0.001 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.03005 ( 117) hydrogen bonds : angle 4.01637 ( 342) SS BOND : bond 0.01056 ( 3) SS BOND : angle 4.16812 ( 6) covalent geometry : bond 0.00400 ( 3614) covalent geometry : angle 0.80643 ( 4896) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.424 Fit side-chains REVERT: A 85 GLU cc_start: 0.7161 (tp30) cc_final: 0.6615 (tt0) REVERT: A 92 TYR cc_start: 0.8815 (p90) cc_final: 0.7856 (p90) REVERT: A 102 HIS cc_start: 0.7433 (m-70) cc_final: 0.6991 (t-90) REVERT: A 114 ASP cc_start: 0.8762 (t70) cc_final: 0.8481 (t0) REVERT: A 198 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8241 (tttt) REVERT: A 211 GLU cc_start: 0.8514 (tp30) cc_final: 0.7994 (mm-30) REVERT: A 302 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7183 (pp20) REVERT: A 358 GLN cc_start: 0.9001 (mm110) cc_final: 0.8409 (tp40) REVERT: A 435 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8407 (pp) REVERT: A 460 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8340 (tm-30) outliers start: 7 outliers final: 4 residues processed: 44 average time/residue: 0.9671 time to fit residues: 44.4432 Evaluate side-chains 44 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 435 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.129392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.101020 restraints weight = 6685.297| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.71 r_work: 0.3375 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3617 Z= 0.180 Angle : 0.840 17.953 4902 Z= 0.408 Chirality : 0.048 0.221 566 Planarity : 0.004 0.043 622 Dihedral : 6.197 35.588 481 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.44 % Allowed : 13.33 % Favored : 86.22 % Rotamer: Outliers : 1.55 % Allowed : 23.26 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.40), residues: 450 helix: 0.80 (0.41), residues: 179 sheet: -1.37 (0.66), residues: 49 loop : -2.75 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 207 HIS 0.007 0.001 HIS A 51 PHE 0.013 0.002 PHE A 356 TYR 0.014 0.002 TYR A 327 ARG 0.006 0.001 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 117) hydrogen bonds : angle 4.03547 ( 342) SS BOND : bond 0.01076 ( 3) SS BOND : angle 4.23704 ( 6) covalent geometry : bond 0.00421 ( 3614) covalent geometry : angle 0.82720 ( 4896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2915.87 seconds wall clock time: 50 minutes 38.47 seconds (3038.47 seconds total)