Starting phenix.real_space_refine on Thu Mar 6 10:08:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdo_17616/03_2025/8pdo_17616.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdo_17616/03_2025/8pdo_17616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pdo_17616/03_2025/8pdo_17616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdo_17616/03_2025/8pdo_17616.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdo_17616/03_2025/8pdo_17616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdo_17616/03_2025/8pdo_17616.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.032 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: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 22 5.16 5 C 3564 2.51 5 N 990 2.21 5 O 1132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 5722 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Chain: "C" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 280 Classifications: {'RNA': 14} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 12} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain: "B" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Time building chain proxies: 4.77, per 1000 atoms: 0.83 Number of scatterers: 5722 At special positions: 0 Unit cell: (114.45, 79.8, 82.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 14 15.00 O 1132 8.00 N 990 7.00 C 3564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 807.5 milliseconds 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1304 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 69.1% alpha, 2.6% beta 0 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 3.595A pdb=" N TYR A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.896A pdb=" N LEU A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 120 through 141 Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 175 through 191 removed outlier: 4.142A pdb=" N ARG A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.846A pdb=" N SER A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 256 through 269 removed outlier: 3.593A pdb=" N ARG A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.821A pdb=" N GLY A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.620A pdb=" N LEU B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 75 Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 120 through 141 Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.584A pdb=" N GLN B 150 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG B 151 " --> pdb=" O GLN B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 151' Processing helix chain 'B' and resid 156 through 171 removed outlier: 3.854A pdb=" N LYS B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 191 removed outlier: 3.846A pdb=" N ARG B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 234 removed outlier: 3.789A pdb=" N SER B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 251 Processing helix chain 'B' and resid 256 through 268 removed outlier: 3.613A pdb=" N ARG B 260 " --> pdb=" O GLN B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 275 through 296 removed outlier: 4.860A pdb=" N LYS B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLN B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 300 removed outlier: 3.890A pdb=" N GLY B 300 " --> pdb=" O PRO B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 318 through 332 Processing helix chain 'B' and resid 344 through 361 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.299A pdb=" N THR A 33 " --> pdb=" O VAL A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.695A pdb=" N ARG A 96 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 35 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 336 hydrogen bonds defined for protein. 987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 1.66 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: 1845 1.34 - 1.46: 846 1.46 - 1.57: 3079 1.57 - 1.69: 27 1.69 - 1.81: 38 Bond restraints: 5835 Sorted by residual: bond pdb=" C VAL A 35 " pdb=" N THR A 36 " ideal model delta sigma weight residual 1.331 1.303 0.027 1.24e-02 6.50e+03 4.88e+00 bond pdb=" CB VAL B 92 " pdb=" CG1 VAL B 92 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.06e+00 bond pdb=" CA GLU B 20 " pdb=" C GLU B 20 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.66e-02 3.63e+03 3.98e+00 bond pdb=" CB VAL A 92 " pdb=" CG1 VAL A 92 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.63e+00 bond pdb=" N LYS B 239 " pdb=" CA LYS B 239 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.33e-02 5.65e+03 2.83e+00 ... (remaining 5830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 7551 1.43 - 2.86: 349 2.86 - 4.29: 31 4.29 - 5.72: 3 5.72 - 7.15: 4 Bond angle restraints: 7938 Sorted by residual: angle pdb=" C LEU A 52 " pdb=" N TYR A 53 " pdb=" CA TYR A 53 " ideal model delta sigma weight residual 122.60 115.45 7.15 1.56e+00 4.11e-01 2.10e+01 angle pdb=" N ILE A 6 " pdb=" CA ILE A 6 " pdb=" C ILE A 6 " ideal model delta sigma weight residual 106.21 108.97 -2.76 1.07e+00 8.73e-01 6.66e+00 angle pdb=" C GLN A 91 " pdb=" N VAL A 92 " pdb=" CA VAL A 92 " ideal model delta sigma weight residual 120.63 123.86 -3.23 1.33e+00 5.65e-01 5.91e+00 angle pdb=" N LYS B 239 " pdb=" CA LYS B 239 " pdb=" C LYS B 239 " ideal model delta sigma weight residual 112.54 109.71 2.83 1.22e+00 6.72e-01 5.38e+00 angle pdb=" CA GLU B 20 " pdb=" C GLU B 20 " pdb=" N SER B 21 " ideal model delta sigma weight residual 117.96 120.71 -2.75 1.23e+00 6.61e-01 4.98e+00 ... (remaining 7933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3187 17.53 - 35.05: 315 35.05 - 52.58: 59 52.58 - 70.11: 13 70.11 - 87.64: 21 Dihedral angle restraints: 3595 sinusoidal: 1563 harmonic: 2032 Sorted by residual: dihedral pdb=" CA GLY B 311 " pdb=" C GLY B 311 " pdb=" N LEU B 312 " pdb=" CA LEU B 312 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA LEU B 52 " pdb=" C LEU B 52 " pdb=" N TYR B 53 " pdb=" CA TYR B 53 " ideal model delta harmonic sigma weight residual -180.00 -162.74 -17.26 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ALA B 251 " pdb=" C ALA B 251 " pdb=" N TYR B 252 " pdb=" CA TYR B 252 " ideal model delta harmonic sigma weight residual -180.00 -163.14 -16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 3592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 652 0.042 - 0.083: 226 0.083 - 0.125: 48 0.125 - 0.166: 8 0.166 - 0.208: 2 Chirality restraints: 936 Sorted by residual: chirality pdb=" CB VAL B 35 " pdb=" CA VAL B 35 " pdb=" CG1 VAL B 35 " pdb=" CG2 VAL B 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB VAL A 35 " pdb=" CA VAL A 35 " pdb=" CG1 VAL A 35 " pdb=" CG2 VAL A 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CA ILE A 25 " pdb=" N ILE A 25 " pdb=" C ILE A 25 " pdb=" CB ILE A 25 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 933 not shown) Planarity restraints: 962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 198 " -0.033 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO A 199 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 199 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 199 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 53 " 0.007 2.00e-02 2.50e+03 1.34e-02 3.60e+00 pdb=" CG TYR A 53 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 53 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 53 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 53 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 53 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 53 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 53 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 73 " 0.025 2.00e-02 2.50e+03 1.25e-02 3.53e+00 pdb=" N1 C C 73 " -0.025 2.00e-02 2.50e+03 pdb=" C2 C C 73 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C C 73 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C C 73 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C C 73 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C C 73 " 0.009 2.00e-02 2.50e+03 pdb=" C5 C C 73 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C C 73 " -0.005 2.00e-02 2.50e+03 ... (remaining 959 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 51 2.63 - 3.20: 5295 3.20 - 3.77: 9054 3.77 - 4.33: 12859 4.33 - 4.90: 20585 Nonbonded interactions: 47844 Sorted by model distance: nonbonded pdb=" O LEU A 18 " pdb=" OG SER B 233 " model vdw 2.068 3.040 nonbonded pdb=" OG SER A 277 " pdb=" OD1 ASN A 320 " model vdw 2.138 3.040 nonbonded pdb=" O VAL A 35 " pdb=" OG1 THR A 95 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR A 338 " pdb=" OP2 C C 74 " model vdw 2.232 3.040 nonbonded pdb=" NH1 ARG A 27 " pdb=" O THR B 236 " model vdw 2.241 3.120 ... (remaining 47839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.180 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.006 0.067 5835 Z= 0.418 Angle : 0.664 7.149 7938 Z= 0.393 Chirality : 0.044 0.208 936 Planarity : 0.004 0.051 962 Dihedral : 15.615 87.636 2291 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.32), residues: 694 helix: 0.59 (0.24), residues: 470 sheet: -1.01 (0.87), residues: 30 loop : -0.60 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 123 HIS 0.004 0.001 HIS B 15 PHE 0.017 0.002 PHE B 224 TYR 0.031 0.003 TYR A 53 ARG 0.008 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.622 Fit side-chains REVERT: A 78 ARG cc_start: 0.7403 (mmm160) cc_final: 0.5880 (tpt-90) REVERT: A 249 MET cc_start: 0.7654 (mmt) cc_final: 0.7430 (mmt) REVERT: A 266 ARG cc_start: 0.7783 (tmt170) cc_final: 0.5836 (tpt170) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2628 time to fit residues: 27.3223 Evaluate side-chains 76 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.0270 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 0.3980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.159989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.139003 restraints weight = 6596.060| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.58 r_work: 0.3432 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5835 Z= 0.202 Angle : 0.483 6.157 7938 Z= 0.262 Chirality : 0.039 0.143 936 Planarity : 0.004 0.046 962 Dihedral : 11.435 74.012 987 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.50 % Allowed : 5.20 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.32), residues: 694 helix: 1.16 (0.24), residues: 474 sheet: -0.94 (0.88), residues: 30 loop : -0.61 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 123 HIS 0.003 0.001 HIS A 275 PHE 0.013 0.001 PHE B 224 TYR 0.018 0.002 TYR A 53 ARG 0.006 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.580 Fit side-chains REVERT: A 78 ARG cc_start: 0.7383 (mmm160) cc_final: 0.5358 (tpt-90) REVERT: A 266 ARG cc_start: 0.7746 (tmt170) cc_final: 0.5589 (tpt170) REVERT: A 337 MET cc_start: 0.8666 (tpp) cc_final: 0.8384 (mmp) REVERT: B 129 LYS cc_start: 0.7277 (pttm) cc_final: 0.7058 (pptt) REVERT: B 196 LYS cc_start: 0.7800 (mttt) cc_final: 0.7519 (ttpp) outliers start: 3 outliers final: 2 residues processed: 78 average time/residue: 0.2748 time to fit residues: 25.8946 Evaluate side-chains 73 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 175 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 70 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.152083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.130213 restraints weight = 6664.167| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.66 r_work: 0.3365 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5835 Z= 0.268 Angle : 0.498 6.198 7938 Z= 0.268 Chirality : 0.040 0.139 936 Planarity : 0.004 0.044 962 Dihedral : 11.437 74.177 987 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.50 % Allowed : 8.56 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.33), residues: 694 helix: 1.18 (0.24), residues: 474 sheet: -1.08 (0.88), residues: 30 loop : -0.49 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 123 HIS 0.003 0.001 HIS B 15 PHE 0.013 0.002 PHE B 224 TYR 0.015 0.002 TYR A 59 ARG 0.006 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.844 Fit side-chains REVERT: A 78 ARG cc_start: 0.7403 (mmm160) cc_final: 0.5337 (tpt-90) REVERT: A 266 ARG cc_start: 0.7802 (tmt170) cc_final: 0.5556 (tpt170) REVERT: B 196 LYS cc_start: 0.7717 (mttt) cc_final: 0.7467 (ttpp) outliers start: 3 outliers final: 3 residues processed: 73 average time/residue: 0.3286 time to fit residues: 29.3068 Evaluate side-chains 71 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain B residue 175 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.153560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.131132 restraints weight = 6797.751| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.67 r_work: 0.3366 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5835 Z= 0.278 Angle : 0.500 6.195 7938 Z= 0.268 Chirality : 0.041 0.200 936 Planarity : 0.004 0.041 962 Dihedral : 11.429 74.174 987 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.01 % Allowed : 9.40 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.33), residues: 694 helix: 1.11 (0.24), residues: 478 sheet: -1.02 (0.89), residues: 30 loop : -0.37 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 123 HIS 0.003 0.001 HIS B 15 PHE 0.013 0.002 PHE B 224 TYR 0.015 0.002 TYR A 59 ARG 0.008 0.001 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.627 Fit side-chains REVERT: A 78 ARG cc_start: 0.7429 (mmm160) cc_final: 0.5367 (tpt-90) REVERT: A 135 MET cc_start: 0.7021 (ttt) cc_final: 0.6760 (ttt) REVERT: A 266 ARG cc_start: 0.7803 (tmt170) cc_final: 0.5565 (tpt170) REVERT: B 196 LYS cc_start: 0.7720 (mttt) cc_final: 0.7458 (ttpp) outliers start: 6 outliers final: 5 residues processed: 75 average time/residue: 0.2959 time to fit residues: 26.6279 Evaluate side-chains 74 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 175 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.155648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.133745 restraints weight = 6640.716| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.63 r_work: 0.3389 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5835 Z= 0.225 Angle : 0.468 6.101 7938 Z= 0.251 Chirality : 0.040 0.162 936 Planarity : 0.004 0.040 962 Dihedral : 11.432 74.009 987 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.01 % Allowed : 11.41 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.33), residues: 694 helix: 1.21 (0.24), residues: 480 sheet: -1.01 (0.88), residues: 30 loop : -0.51 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 123 HIS 0.003 0.001 HIS A 7 PHE 0.012 0.001 PHE B 224 TYR 0.012 0.002 TYR A 59 ARG 0.007 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.620 Fit side-chains REVERT: A 78 ARG cc_start: 0.7376 (mmm160) cc_final: 0.5312 (tpt-90) REVERT: A 135 MET cc_start: 0.6895 (ttt) cc_final: 0.6659 (ttt) REVERT: A 266 ARG cc_start: 0.7699 (tmt170) cc_final: 0.4681 (mtt180) REVERT: B 129 LYS cc_start: 0.7369 (pttm) cc_final: 0.7167 (pptt) REVERT: B 139 LEU cc_start: 0.8150 (tp) cc_final: 0.7788 (tt) REVERT: B 196 LYS cc_start: 0.7693 (mttt) cc_final: 0.7389 (ttpp) outliers start: 6 outliers final: 3 residues processed: 76 average time/residue: 0.3047 time to fit residues: 27.9913 Evaluate side-chains 72 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 341 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 46 optimal weight: 0.0270 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.154370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.132218 restraints weight = 6661.505| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.66 r_work: 0.3390 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5835 Z= 0.210 Angle : 0.459 6.062 7938 Z= 0.247 Chirality : 0.039 0.152 936 Planarity : 0.004 0.040 962 Dihedral : 11.449 74.074 987 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.17 % Allowed : 12.42 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.33), residues: 694 helix: 1.30 (0.24), residues: 480 sheet: -1.04 (0.88), residues: 30 loop : -0.53 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 PHE 0.011 0.001 PHE B 224 TYR 0.012 0.002 TYR A 59 ARG 0.008 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.605 Fit side-chains REVERT: A 78 ARG cc_start: 0.7369 (mmm160) cc_final: 0.5309 (tpt-90) REVERT: A 135 MET cc_start: 0.7003 (ttt) cc_final: 0.6711 (ttt) REVERT: A 266 ARG cc_start: 0.7720 (tmt170) cc_final: 0.4679 (mtt180) REVERT: A 284 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7255 (tm-30) REVERT: B 139 LEU cc_start: 0.8222 (tp) cc_final: 0.7837 (tt) REVERT: B 196 LYS cc_start: 0.7654 (mttt) cc_final: 0.7385 (ttpp) REVERT: B 282 LEU cc_start: 0.8632 (mt) cc_final: 0.8365 (mt) outliers start: 7 outliers final: 4 residues processed: 78 average time/residue: 0.3683 time to fit residues: 34.5730 Evaluate side-chains 77 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 341 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 60 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.2980 chunk 66 optimal weight: 0.0870 chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.156396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.134529 restraints weight = 6608.712| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.64 r_work: 0.3407 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5835 Z= 0.208 Angle : 0.457 6.043 7938 Z= 0.246 Chirality : 0.039 0.142 936 Planarity : 0.004 0.040 962 Dihedral : 11.461 74.048 987 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.84 % Allowed : 13.59 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.33), residues: 694 helix: 1.33 (0.24), residues: 480 sheet: -1.08 (0.88), residues: 30 loop : -0.53 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 PHE 0.011 0.001 PHE B 224 TYR 0.012 0.001 TYR A 59 ARG 0.009 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.727 Fit side-chains REVERT: A 36 THR cc_start: 0.8359 (m) cc_final: 0.8138 (m) REVERT: A 78 ARG cc_start: 0.7379 (mmm160) cc_final: 0.5324 (tpt-90) REVERT: A 135 MET cc_start: 0.7032 (ttt) cc_final: 0.6735 (ttt) REVERT: A 266 ARG cc_start: 0.7713 (tmt170) cc_final: 0.4680 (mtt180) REVERT: A 284 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7219 (tm-30) REVERT: B 196 LYS cc_start: 0.7617 (mttt) cc_final: 0.7379 (ttpp) REVERT: B 282 LEU cc_start: 0.8636 (mt) cc_final: 0.8373 (mt) outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 0.3102 time to fit residues: 28.8411 Evaluate side-chains 75 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 341 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 0.0270 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 0.0010 chunk 0 optimal weight: 1.9990 overall best weight: 0.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.168745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.150098 restraints weight = 6470.178| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.31 r_work: 0.3258 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5835 Z= 0.191 Angle : 0.449 6.024 7938 Z= 0.241 Chirality : 0.039 0.182 936 Planarity : 0.004 0.039 962 Dihedral : 11.470 73.986 987 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.84 % Allowed : 13.59 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.33), residues: 694 helix: 1.45 (0.25), residues: 476 sheet: -0.94 (0.91), residues: 30 loop : -0.27 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 PHE 0.010 0.001 PHE B 224 TYR 0.012 0.001 TYR A 338 ARG 0.009 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.595 Fit side-chains REVERT: A 36 THR cc_start: 0.8229 (m) cc_final: 0.8007 (m) REVERT: A 78 ARG cc_start: 0.7472 (mmm160) cc_final: 0.5498 (tpt-90) REVERT: A 135 MET cc_start: 0.6973 (ttt) cc_final: 0.6666 (ttt) REVERT: A 266 ARG cc_start: 0.7736 (tmt170) cc_final: 0.4800 (mtt180) REVERT: B 117 HIS cc_start: 0.7147 (t70) cc_final: 0.6654 (t70) REVERT: B 139 LEU cc_start: 0.8232 (tp) cc_final: 0.7999 (tt) outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 0.2534 time to fit residues: 23.9937 Evaluate side-chains 75 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 341 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 68 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 66 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 0.0470 chunk 29 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.168032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.149259 restraints weight = 6512.047| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.32 r_work: 0.3558 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5835 Z= 0.207 Angle : 0.459 6.055 7938 Z= 0.246 Chirality : 0.039 0.173 936 Planarity : 0.004 0.039 962 Dihedral : 11.473 74.038 987 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.67 % Allowed : 14.09 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.33), residues: 694 helix: 1.43 (0.24), residues: 480 sheet: -0.93 (0.92), residues: 30 loop : -0.49 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 PHE 0.011 0.001 PHE B 224 TYR 0.012 0.001 TYR A 59 ARG 0.010 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.638 Fit side-chains REVERT: A 36 THR cc_start: 0.8236 (m) cc_final: 0.8016 (m) REVERT: A 78 ARG cc_start: 0.7575 (mmm160) cc_final: 0.5675 (tpt-90) REVERT: A 135 MET cc_start: 0.7009 (ttt) cc_final: 0.6762 (ttt) REVERT: A 266 ARG cc_start: 0.7805 (tmt170) cc_final: 0.4805 (mtt180) REVERT: A 284 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7626 (tm-30) REVERT: B 117 HIS cc_start: 0.7248 (t70) cc_final: 0.6763 (t70) outliers start: 4 outliers final: 2 residues processed: 75 average time/residue: 0.2541 time to fit residues: 23.5917 Evaluate side-chains 73 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.167300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.148133 restraints weight = 6619.553| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.36 r_work: 0.3551 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5835 Z= 0.232 Angle : 0.473 6.085 7938 Z= 0.254 Chirality : 0.040 0.192 936 Planarity : 0.004 0.040 962 Dihedral : 11.473 74.047 987 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.67 % Allowed : 14.43 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.33), residues: 694 helix: 1.39 (0.24), residues: 480 sheet: -1.51 (0.75), residues: 38 loop : -0.39 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 PHE 0.012 0.001 PHE B 224 TYR 0.013 0.002 TYR A 59 ARG 0.011 0.001 ARG B 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1388 Ramachandran restraints generated. 694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.604 Fit side-chains REVERT: A 36 THR cc_start: 0.8245 (m) cc_final: 0.8024 (m) REVERT: A 78 ARG cc_start: 0.7604 (mmm160) cc_final: 0.5706 (tpt-90) REVERT: A 135 MET cc_start: 0.6995 (ttt) cc_final: 0.6750 (ttt) REVERT: A 266 ARG cc_start: 0.7840 (tmt170) cc_final: 0.4835 (mtt180) REVERT: A 284 GLN cc_start: 0.7894 (tm-30) cc_final: 0.7592 (tm-30) REVERT: B 117 HIS cc_start: 0.7304 (t70) cc_final: 0.6801 (t70) REVERT: B 282 LEU cc_start: 0.8653 (mt) cc_final: 0.8435 (mt) outliers start: 4 outliers final: 3 residues processed: 72 average time/residue: 0.2598 time to fit residues: 23.0356 Evaluate side-chains 73 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 341 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 25 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 HIS ** B 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.155802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.133993 restraints weight = 6841.076| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.59 r_work: 0.3444 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5835 Z= 0.214 Angle : 0.465 6.087 7938 Z= 0.250 Chirality : 0.040 0.173 936 Planarity : 0.004 0.039 962 Dihedral : 11.478 74.014 987 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.84 % Allowed : 14.43 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.33), residues: 694 helix: 1.45 (0.24), residues: 480 sheet: -1.10 (0.91), residues: 30 loop : -0.48 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 123 HIS 0.002 0.001 HIS A 7 PHE 0.011 0.001 PHE B 224 TYR 0.012 0.002 TYR A 338 ARG 0.010 0.000 ARG B 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3382.11 seconds wall clock time: 60 minutes 15.31 seconds (3615.31 seconds total)