Starting phenix.real_space_refine on Wed Mar 5 20:58:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sib_40505/03_2025/8sib_40505.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sib_40505/03_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_40505/03_2025/8sib_40505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sib_40505/03_2025/8sib_40505.map" model { file = "/net/cci-nas-00/data/ceres_data/8sib_40505/03_2025/8sib_40505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sib_40505/03_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-5624/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: 2.93, per 1000 atoms: 0.83 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: 0.79 Conformation dependent library (CDL) restraints added in 423.7 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: 0.34 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: 0.78 Time building geometry restraints manager: 0.97 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: 1.210 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.670 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:10.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.580 ------------------------------------------------------------------------------- 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 3614 Z= 0.439 Angle : 1.304 13.305 4896 Z= 0.754 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 *********************** 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 : 0.397 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: 1.3101 time to fit residues: 107.7609 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 : 0.370 ------------------------------------------------------------------------------- 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 3614 Z= 0.250 Angle : 0.833 11.468 4896 Z= 0.424 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 *********************** 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 : 0.374 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: 1.2125 time to fit residues: 76.4033 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 : 0.407 ------------------------------------------------------------------------------- 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: 0.0670 chunk 36 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.124562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.094323 restraints weight = 6248.867| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.62 r_work: 0.3310 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3614 Z= 0.274 Angle : 0.846 14.946 4896 Z= 0.416 Chirality : 0.047 0.177 566 Planarity : 0.004 0.041 622 Dihedral : 7.122 44.716 481 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.89 % Allowed : 12.89 % Favored : 86.22 % 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: -2.61 (0.37), residues: 450 helix: -0.17 (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 0.008 0.001 TYR A 327 ARG 0.007 0.001 ARG A 46 *********************** 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 : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7203 (tp30) cc_final: 0.6621 (tt0) REVERT: A 102 HIS cc_start: 0.7275 (m-70) cc_final: 0.6882 (t-90) REVERT: A 131 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8133 (mm-30) REVERT: A 198 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8284 (tttt) REVERT: A 211 GLU cc_start: 0.8525 (tp30) cc_final: 0.8150 (mm-30) REVERT: A 291 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: A 340 ASP cc_start: 0.8796 (t70) cc_final: 0.8574 (p0) REVERT: A 460 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8246 (tm-30) outliers start: 11 outliers final: 3 residues processed: 50 average time/residue: 1.2908 time to fit residues: 66.6658 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 : 0.454 ------------------------------------------------------------------------------- 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: 3.9990 chunk 16 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 0.0870 chunk 21 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.127088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.096987 restraints weight = 6362.147| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.72 r_work: 0.3331 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3614 Z= 0.241 Angle : 0.793 15.435 4896 Z= 0.394 Chirality : 0.047 0.229 566 Planarity : 0.004 0.041 622 Dihedral : 6.764 39.834 481 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.67 % Allowed : 12.44 % Favored : 86.89 % Rotamer: Outliers : 3.88 % Allowed : 13.18 % Favored : 82.95 % 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: -2.15 (0.38), residues: 450 helix: 0.35 (0.40), residues: 178 sheet: -1.89 (0.61), residues: 51 loop : -2.94 (0.38), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 207 HIS 0.005 0.001 HIS A 51 PHE 0.007 0.001 PHE A 146 TYR 0.005 0.001 TYR A 327 ARG 0.004 0.001 ARG A 28 *********************** 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 61 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7156 (tp30) cc_final: 0.6616 (tt0) REVERT: A 92 TYR cc_start: 0.8830 (p90) cc_final: 0.7737 (p90) REVERT: A 102 HIS cc_start: 0.7200 (m-70) cc_final: 0.6878 (t-90) REVERT: A 131 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8136 (mm-30) REVERT: A 198 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8291 (tttt) REVERT: A 211 GLU cc_start: 0.8513 (tp30) cc_final: 0.8184 (mm-30) REVERT: A 291 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: A 340 ASP cc_start: 0.8818 (t70) cc_final: 0.8550 (p0) REVERT: A 460 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8301 (tm-30) outliers start: 15 outliers final: 6 residues processed: 57 average time/residue: 1.0594 time to fit residues: 62.6503 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 : 0.428 ------------------------------------------------------------------------------- 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 291 GLU 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: 0.2980 chunk 5 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.122670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.092192 restraints weight = 6394.272| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.70 r_work: 0.3267 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3614 Z= 0.244 Angle : 0.803 17.118 4896 Z= 0.390 Chirality : 0.047 0.216 566 Planarity : 0.005 0.080 622 Dihedral : 6.599 39.106 481 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.67 % Allowed : 13.33 % Favored : 86.00 % Rotamer: Outliers : 3.88 % Allowed : 15.76 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -1.91 (0.39), residues: 450 helix: 0.57 (0.41), residues: 178 sheet: -1.80 (0.61), residues: 51 loop : -2.81 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 207 HIS 0.004 0.001 HIS A 191 PHE 0.007 0.001 PHE A 454 TYR 0.009 0.001 TYR A 327 ARG 0.003 0.000 ARG A 28 *********************** 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: 15 poor density : 42 time to evaluate : 0.416 Fit side-chains REVERT: A 85 GLU cc_start: 0.7189 (tp30) cc_final: 0.6647 (tt0) REVERT: A 92 TYR cc_start: 0.8850 (p90) cc_final: 0.7714 (p90) REVERT: A 102 HIS cc_start: 0.7289 (m-70) cc_final: 0.6927 (t-90) REVERT: A 131 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8174 (mm-30) REVERT: A 198 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8287 (tttt) REVERT: A 211 GLU cc_start: 0.8494 (tp30) cc_final: 0.8263 (mm-30) REVERT: A 302 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7177 (pp20) REVERT: A 340 ASP cc_start: 0.8800 (t70) cc_final: 0.8585 (p0) REVERT: A 352 LYS cc_start: 0.9161 (mtmm) cc_final: 0.8605 (mtmt) REVERT: A 358 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8555 (mm110) REVERT: A 460 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8357 (tm-30) outliers start: 15 outliers final: 6 residues processed: 53 average time/residue: 1.0714 time to fit residues: 58.9564 Evaluate side-chains 46 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 214 ASN 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: 1.9990 chunk 44 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 33 optimal weight: 0.0270 chunk 41 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 A 240 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.125002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.093638 restraints weight = 6433.165| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.75 r_work: 0.3260 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3614 Z= 0.211 Angle : 0.778 17.775 4896 Z= 0.379 Chirality : 0.046 0.200 566 Planarity : 0.004 0.068 622 Dihedral : 6.392 37.403 481 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.67 % Allowed : 12.22 % Favored : 87.11 % Rotamer: Outliers : 3.62 % Allowed : 17.31 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -1.65 (0.40), residues: 450 helix: 0.77 (0.41), residues: 179 sheet: -1.37 (0.66), residues: 49 loop : -2.74 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 207 HIS 0.004 0.001 HIS A 191 PHE 0.008 0.001 PHE A 381 TYR 0.006 0.001 TYR A 92 ARG 0.003 0.000 ARG A 46 *********************** 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 59 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.412 Fit side-chains REVERT: A 85 GLU cc_start: 0.7302 (tp30) cc_final: 0.6770 (tt0) REVERT: A 92 TYR cc_start: 0.8911 (p90) cc_final: 0.7748 (p90) REVERT: A 102 HIS cc_start: 0.7339 (m-70) cc_final: 0.6987 (t-90) REVERT: A 198 LYS cc_start: 0.8758 (mmtt) cc_final: 0.8289 (tttt) REVERT: A 302 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7370 (pp20) REVERT: A 340 ASP cc_start: 0.8728 (t70) cc_final: 0.8510 (p0) REVERT: A 358 GLN cc_start: 0.8832 (mm-40) cc_final: 0.8560 (mm110) REVERT: A 435 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8579 (pp) REVERT: A 460 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8352 (tm-30) outliers start: 14 outliers final: 6 residues processed: 56 average time/residue: 1.1192 time to fit residues: 64.9077 Evaluate side-chains 49 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 43 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.119614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.088064 restraints weight = 6413.071| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.72 r_work: 0.3231 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 3614 Z= 0.405 Angle : 0.881 18.711 4896 Z= 0.430 Chirality : 0.049 0.206 566 Planarity : 0.005 0.062 622 Dihedral : 6.627 40.014 481 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.67 % Allowed : 14.00 % Favored : 85.33 % Rotamer: Outliers : 3.62 % Allowed : 19.12 % Favored : 77.26 % 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: -1.95 (0.39), residues: 450 helix: 0.46 (0.40), residues: 179 sheet: -1.51 (0.68), residues: 48 loop : -2.85 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 207 HIS 0.006 0.001 HIS A 191 PHE 0.015 0.002 PHE A 454 TYR 0.010 0.002 TYR A 327 ARG 0.003 0.001 ARG A 419 *********************** 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 57 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.371 Fit side-chains REVERT: A 85 GLU cc_start: 0.7421 (tp30) cc_final: 0.6889 (tt0) REVERT: A 102 HIS cc_start: 0.7508 (m-70) cc_final: 0.6999 (t-90) REVERT: A 198 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8283 (tttt) REVERT: A 358 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8710 (mm110) REVERT: A 460 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8378 (tm-30) outliers start: 14 outliers final: 5 residues processed: 54 average time/residue: 1.0025 time to fit residues: 56.3015 Evaluate side-chains 45 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 303 TYR Chi-restraints excluded: chain A residue 371 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 5 optimal weight: 0.0370 chunk 1 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 8.9990 chunk 40 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.0570 chunk 33 optimal weight: 0.8980 overall best weight: 0.2776 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.131873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.103701 restraints weight = 6637.658| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 3.69 r_work: 0.3362 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3614 Z= 0.190 Angle : 0.815 18.984 4896 Z= 0.399 Chirality : 0.047 0.166 566 Planarity : 0.004 0.050 622 Dihedral : 6.317 32.167 481 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.67 % Allowed : 12.67 % Favored : 86.67 % Rotamer: Outliers : 3.10 % Allowed : 19.90 % Favored : 77.00 % 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: -1.56 (0.40), residues: 450 helix: 0.87 (0.41), residues: 179 sheet: -1.25 (0.67), residues: 49 loop : -2.74 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 6 HIS 0.007 0.001 HIS A 149 PHE 0.007 0.001 PHE A 146 TYR 0.008 0.001 TYR A 92 ARG 0.003 0.000 ARG A 46 *********************** 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 59 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.474 Fit side-chains REVERT: A 85 GLU cc_start: 0.7185 (tp30) cc_final: 0.6654 (tt0) REVERT: A 92 TYR cc_start: 0.8868 (p90) cc_final: 0.7709 (p90) REVERT: A 102 HIS cc_start: 0.7355 (m-70) cc_final: 0.6963 (t-90) REVERT: A 114 ASP cc_start: 0.8702 (t70) cc_final: 0.8421 (t0) REVERT: A 151 ARG cc_start: 0.8732 (tpt170) cc_final: 0.8336 (tpt170) REVERT: A 198 LYS cc_start: 0.8707 (mmtt) cc_final: 0.8237 (tttt) REVERT: A 211 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7631 (mm-30) REVERT: A 302 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7318 (pp20) REVERT: A 358 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8634 (mm110) REVERT: A 460 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8355 (tm-30) outliers start: 12 outliers final: 8 residues processed: 55 average time/residue: 1.0062 time to fit residues: 57.6036 Evaluate side-chains 51 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 302 GLU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.128941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.100485 restraints weight = 6622.388| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.68 r_work: 0.3368 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3614 Z= 0.291 Angle : 0.853 20.142 4896 Z= 0.416 Chirality : 0.048 0.182 566 Planarity : 0.005 0.048 622 Dihedral : 6.247 33.281 481 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.67 % Allowed : 13.56 % Favored : 85.78 % Rotamer: Outliers : 2.84 % Allowed : 20.41 % Favored : 76.74 % 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: -1.66 (0.40), residues: 450 helix: 0.81 (0.41), residues: 179 sheet: -1.35 (0.66), residues: 49 loop : -2.79 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 207 HIS 0.004 0.001 HIS A 191 PHE 0.011 0.002 PHE A 454 TYR 0.013 0.001 TYR A 327 ARG 0.004 0.000 ARG A 419 *********************** 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 53 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.382 Fit side-chains REVERT: A 85 GLU cc_start: 0.7284 (tp30) cc_final: 0.6763 (tt0) REVERT: A 92 TYR cc_start: 0.8853 (p90) cc_final: 0.7585 (p90) REVERT: A 102 HIS cc_start: 0.7456 (m-70) cc_final: 0.6953 (t-90) REVERT: A 114 ASP cc_start: 0.8778 (t70) cc_final: 0.8475 (t0) REVERT: A 198 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8252 (tttt) REVERT: A 302 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7391 (pp20) REVERT: A 358 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8717 (mm110) REVERT: A 460 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8354 (tm-30) outliers start: 11 outliers final: 8 residues processed: 50 average time/residue: 0.9343 time to fit residues: 48.8239 Evaluate side-chains 48 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 155 LEU Chi-restraints excluded: chain A residue 214 ASN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.129644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.101218 restraints weight = 6710.621| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.70 r_work: 0.3317 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3614 Z= 0.255 Angle : 0.866 20.315 4896 Z= 0.417 Chirality : 0.048 0.192 566 Planarity : 0.004 0.043 622 Dihedral : 6.234 34.000 481 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.67 % Allowed : 13.11 % Favored : 86.22 % Rotamer: Outliers : 2.58 % Allowed : 20.93 % Favored : 76.49 % 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: -1.62 (0.40), residues: 450 helix: 0.86 (0.41), residues: 179 sheet: -1.31 (0.66), residues: 49 loop : -2.80 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 207 HIS 0.004 0.001 HIS A 191 PHE 0.020 0.001 PHE A 356 TYR 0.006 0.001 TYR A 108 ARG 0.004 0.000 ARG A 419 ********************** 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 51 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.402 Fit side-chains REVERT: A 85 GLU cc_start: 0.7227 (tp30) cc_final: 0.6685 (tt0) REVERT: A 92 TYR cc_start: 0.8860 (p90) cc_final: 0.7609 (p90) REVERT: A 102 HIS cc_start: 0.7473 (m-70) cc_final: 0.6965 (t-90) REVERT: A 114 ASP cc_start: 0.8782 (t70) cc_final: 0.8499 (t0) REVERT: A 151 ARG cc_start: 0.8580 (tpt170) cc_final: 0.8282 (tpm170) REVERT: A 198 LYS cc_start: 0.8730 (mmtt) cc_final: 0.8237 (tttt) REVERT: A 302 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7335 (pp20) REVERT: A 358 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8735 (mm110) REVERT: A 460 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8346 (tm-30) outliers start: 10 outliers final: 4 residues processed: 50 average time/residue: 0.9676 time to fit residues: 50.4871 Evaluate side-chains 45 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 30 optimal weight: 0.0670 chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.128612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.099972 restraints weight = 6704.283| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.72 r_work: 0.3364 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3614 Z= 0.298 Angle : 0.888 20.513 4896 Z= 0.425 Chirality : 0.050 0.264 566 Planarity : 0.004 0.045 622 Dihedral : 6.274 33.871 481 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.67 % Allowed : 13.56 % Favored : 85.78 % Rotamer: Outliers : 2.33 % Allowed : 21.19 % Favored : 76.49 % 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: -1.70 (0.40), residues: 450 helix: 0.76 (0.41), residues: 179 sheet: -1.31 (0.66), residues: 49 loop : -2.83 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 207 HIS 0.004 0.001 HIS A 191 PHE 0.016 0.002 PHE A 356 TYR 0.014 0.002 TYR A 327 ARG 0.004 0.001 ARG A 419 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2879.81 seconds wall clock time: 49 minutes 52.76 seconds (2992.76 seconds total)