Starting phenix.real_space_refine on Sat Apr 26 18:13:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cog_16776/04_2025/8cog_16776.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cog_16776/04_2025/8cog_16776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.499 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cog_16776/04_2025/8cog_16776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cog_16776/04_2025/8cog_16776.map" model { file = "/net/cci-nas-00/data/ceres_data/8cog_16776/04_2025/8cog_16776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cog_16776/04_2025/8cog_16776.cif" } resolution = 3.499 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= 0.005 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 22 5.16 5 C 1858 2.51 5 N 498 2.21 5 O 568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 2949 Number of models: 1 Model: "" Number of chains: 2 Chain: "F" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2921 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 354} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.66, per 1000 atoms: 0.90 Number of scatterers: 2949 At special positions: 0 Unit cell: (79.92, 62.64, 82.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 2 15.00 Mg 1 11.99 O 568 8.00 N 498 7.00 C 1858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 216 " - pdb=" SG CYS F 256 " distance=2.10 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: 0.75 Conformation dependent library (CDL) restraints added in 359.5 milliseconds 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 692 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 6 sheets defined 45.7% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'F' and resid 54 through 60 removed outlier: 4.060A pdb=" N GLN F 58 " --> pdb=" O GLY F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 91 Processing helix chain 'F' and resid 111 through 125 removed outlier: 4.157A pdb=" N ARG F 115 " --> pdb=" O PRO F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 145 Processing helix chain 'F' and resid 171 through 174 Processing helix chain 'F' and resid 180 through 193 removed outlier: 3.554A pdb=" N LYS F 190 " --> pdb=" O ASP F 186 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR F 193 " --> pdb=" O MET F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 216 Processing helix chain 'F' and resid 221 through 232 Processing helix chain 'F' and resid 250 through 255 Processing helix chain 'F' and resid 256 through 262 removed outlier: 4.021A pdb=" N ALA F 259 " --> pdb=" O CYS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 282 Processing helix chain 'F' and resid 285 through 294 removed outlier: 4.201A pdb=" N LYS F 290 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASP F 291 " --> pdb=" O ASP F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 320 removed outlier: 3.582A pdb=" N LYS F 314 " --> pdb=" O ASP F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 335 No H-bonds generated for 'chain 'F' and resid 333 through 335' Processing helix chain 'F' and resid 336 through 348 Processing helix chain 'F' and resid 358 through 365 removed outlier: 3.802A pdb=" N GLU F 363 " --> pdb=" O GLN F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing sheet with id=AA1, first strand: chain 'F' and resid 16 through 17 removed outlier: 4.125A pdb=" N LYS F 17 " --> pdb=" O ASP F 10 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASN F 11 " --> pdb=" O THR F 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.518A pdb=" N GLY F 35 " --> pdb=" O TYR F 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 70 through 71 Processing sheet with id=AA4, first strand: chain 'F' and resid 168 through 169 Processing sheet with id=AA5, first strand: chain 'F' and resid 168 through 169 Processing sheet with id=AA6, first strand: chain 'F' and resid 237 through 240 140 hydrogen bonds defined for protein. 366 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: 0.82 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.06: 1 1.06 - 1.25: 329 1.25 - 1.45: 949 1.45 - 1.64: 1696 1.64 - 1.84: 38 Bond restraints: 3013 Sorted by residual: bond pdb=" C PHE F 374 " pdb=" O PHE F 374 " ideal model delta sigma weight residual 1.231 0.861 0.370 2.00e-02 2.50e+03 3.43e+02 bond pdb=" C PHE F 374 " pdb=" OXT PHE F 374 " ideal model delta sigma weight residual 1.231 1.547 -0.316 2.00e-02 2.50e+03 2.50e+02 bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.392 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" N ALA F 330 " pdb=" CA ALA F 330 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.10e-03 1.98e+04 1.99e+01 bond pdb=" N VAL F 162 " pdb=" CA VAL F 162 " ideal model delta sigma weight residual 1.456 1.493 -0.037 8.70e-03 1.32e+04 1.80e+01 ... (remaining 3008 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 3978 4.44 - 8.88: 99 8.88 - 13.32: 9 13.32 - 17.76: 0 17.76 - 22.20: 1 Bond angle restraints: 4087 Sorted by residual: angle pdb=" CA PHE F 374 " pdb=" C PHE F 374 " pdb=" OXT PHE F 374 " ideal model delta sigma weight residual 121.00 98.80 22.20 3.00e+00 1.11e-01 5.48e+01 angle pdb=" C PRO F 242 " pdb=" N ASP F 243 " pdb=" CA ASP F 243 " ideal model delta sigma weight residual 120.28 128.35 -8.07 1.44e+00 4.82e-01 3.14e+01 angle pdb=" CA PHE F 261 " pdb=" C PHE F 261 " pdb=" O PHE F 261 " ideal model delta sigma weight residual 119.38 112.89 6.49 1.23e+00 6.61e-01 2.78e+01 angle pdb=" N HIS F 274 " pdb=" CA HIS F 274 " pdb=" C HIS F 274 " ideal model delta sigma weight residual 111.69 105.95 5.74 1.23e+00 6.61e-01 2.18e+01 angle pdb=" N LYS F 283 " pdb=" CA LYS F 283 " pdb=" C LYS F 283 " ideal model delta sigma weight residual 113.23 107.48 5.75 1.24e+00 6.50e-01 2.15e+01 ... (remaining 4082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.00: 1686 25.00 - 50.01: 98 50.01 - 75.01: 28 75.01 - 100.02: 4 100.02 - 125.02: 1 Dihedral angle restraints: 1817 sinusoidal: 737 harmonic: 1080 Sorted by residual: dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual 300.00 174.97 125.02 1 2.00e+01 2.50e-03 3.78e+01 dihedral pdb=" CA ARG F 27 " pdb=" C ARG F 27 " pdb=" N ALA F 28 " pdb=" CA ALA F 28 " ideal model delta harmonic sigma weight residual -180.00 -154.60 -25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ARG F 195 " pdb=" C ARG F 195 " pdb=" N GLY F 196 " pdb=" CA GLY F 196 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 1814 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.056: 188 0.056 - 0.112: 153 0.112 - 0.168: 81 0.168 - 0.223: 24 0.223 - 0.279: 7 Chirality restraints: 453 Sorted by residual: chirality pdb=" CA VAL F 9 " pdb=" N VAL F 9 " pdb=" C VAL F 9 " pdb=" CB VAL F 9 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA ILE F 249 " pdb=" N ILE F 249 " pdb=" C ILE F 249 " pdb=" CB ILE F 249 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA VAL F 8 " pdb=" N VAL F 8 " pdb=" C VAL F 8 " pdb=" CB VAL F 8 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 450 not shown) Planarity restraints: 523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP F 401 " 0.092 2.00e-02 2.50e+03 3.97e-02 4.33e+01 pdb=" C2 ADP F 401 " -0.039 2.00e-02 2.50e+03 pdb=" C4 ADP F 401 " -0.008 2.00e-02 2.50e+03 pdb=" C5 ADP F 401 " -0.004 2.00e-02 2.50e+03 pdb=" C6 ADP F 401 " 0.008 2.00e-02 2.50e+03 pdb=" C8 ADP F 401 " -0.042 2.00e-02 2.50e+03 pdb=" N1 ADP F 401 " 0.004 2.00e-02 2.50e+03 pdb=" N3 ADP F 401 " -0.007 2.00e-02 2.50e+03 pdb=" N6 ADP F 401 " 0.057 2.00e-02 2.50e+03 pdb=" N7 ADP F 401 " -0.022 2.00e-02 2.50e+03 pdb=" N9 ADP F 401 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 374 " 0.021 2.00e-02 2.50e+03 5.21e-02 2.72e+01 pdb=" C PHE F 374 " -0.088 2.00e-02 2.50e+03 pdb=" O PHE F 374 " 0.048 2.00e-02 2.50e+03 pdb=" OXT PHE F 374 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 30 " -0.041 2.00e-02 2.50e+03 2.77e-02 1.35e+01 pdb=" CG PHE F 30 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE F 30 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE F 30 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE F 30 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE F 30 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE F 30 " -0.042 2.00e-02 2.50e+03 ... (remaining 520 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 799 2.86 - 3.37: 3094 3.37 - 3.88: 4750 3.88 - 4.39: 5826 4.39 - 4.90: 9265 Nonbonded interactions: 23734 Sorted by model distance: nonbonded pdb=" O ILE F 121 " pdb=" OG1 THR F 125 " model vdw 2.346 3.040 nonbonded pdb=" OG SER F 13 " pdb=" O ASP F 156 " model vdw 2.417 3.040 nonbonded pdb=" O2B ADP F 401 " pdb="MG MG F 402 " model vdw 2.435 2.170 nonbonded pdb=" OG1 THR F 148 " pdb=" N GLU F 166 " model vdw 2.438 3.120 nonbonded pdb=" O2' ADP F 401 " pdb=" O3' ADP F 401 " model vdw 2.443 2.432 ... (remaining 23729 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=0.00 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: 0.800 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.530 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.017 0.370 3014 Z= 1.141 Angle : 2.048 22.203 4089 Z= 1.412 Chirality : 0.094 0.279 453 Planarity : 0.008 0.052 523 Dihedral : 17.629 125.023 1122 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.22 % Allowed : 11.71 % Favored : 86.08 % Cbeta Deviations : 0.29 % 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: -2.96 (0.39), residues: 369 helix: -2.12 (0.36), residues: 144 sheet: -0.10 (0.83), residues: 35 loop : -2.20 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.012 TRP F 78 HIS 0.010 0.004 HIS F 86 PHE 0.042 0.010 PHE F 30 TYR 0.041 0.009 TYR F 68 ARG 0.025 0.003 ARG F 311 Details of bonding type rmsd hydrogen bonds : bond 0.27929 ( 138) hydrogen bonds : angle 9.74922 ( 366) SS BOND : bond 0.06635 ( 1) SS BOND : angle 5.79690 ( 2) covalent geometry : bond 0.01700 ( 3013) covalent geometry : angle 2.04416 ( 4087) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: F 4 ILE cc_start: 0.8449 (pt) cc_final: 0.8141 (mt) REVERT: F 11 ASN cc_start: 0.9091 (t0) cc_final: 0.8705 (p0) REVERT: F 40 GLN cc_start: 0.7500 (mt0) cc_final: 0.7162 (pm20) REVERT: F 156 ASP cc_start: 0.8848 (t0) cc_final: 0.8255 (t0) REVERT: F 240 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7353 (pp20) REVERT: F 313 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7475 (tp40) outliers start: 7 outliers final: 0 residues processed: 89 average time/residue: 0.2003 time to fit residues: 20.7762 Evaluate side-chains 52 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.131290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115699 restraints weight = 4113.264| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.79 r_work: 0.3224 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3014 Z= 0.172 Angle : 0.721 7.742 4089 Z= 0.366 Chirality : 0.049 0.311 453 Planarity : 0.005 0.039 523 Dihedral : 8.584 113.234 420 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.16 % Allowed : 16.77 % Favored : 80.06 % 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: -1.50 (0.41), residues: 369 helix: -0.34 (0.39), residues: 155 sheet: -1.03 (0.64), residues: 65 loop : -1.55 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 85 HIS 0.004 0.001 HIS F 160 PHE 0.014 0.002 PHE F 261 TYR 0.016 0.002 TYR F 293 ARG 0.004 0.001 ARG F 195 Details of bonding type rmsd hydrogen bonds : bond 0.04775 ( 138) hydrogen bonds : angle 5.26248 ( 366) SS BOND : bond 0.00015 ( 1) SS BOND : angle 1.04175 ( 2) covalent geometry : bond 0.00404 ( 3013) covalent geometry : angle 0.72034 ( 4087) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.313 Fit side-chains REVERT: F 4 ILE cc_start: 0.8182 (pt) cc_final: 0.7861 (mt) REVERT: F 136 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8329 (mm-40) REVERT: F 142 TYR cc_start: 0.8575 (m-80) cc_final: 0.8348 (m-80) REVERT: F 324 MET cc_start: 0.3663 (OUTLIER) cc_final: 0.3356 (tpp) outliers start: 10 outliers final: 5 residues processed: 68 average time/residue: 0.1136 time to fit residues: 9.9520 Evaluate side-chains 54 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 136 GLN Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 256 CYS Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 348 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 9 optimal weight: 0.0870 chunk 33 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 120 GLN F 136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.116250 restraints weight = 4071.042| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.76 r_work: 0.3226 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3014 Z= 0.127 Angle : 0.650 8.551 4089 Z= 0.322 Chirality : 0.044 0.143 453 Planarity : 0.004 0.039 523 Dihedral : 7.832 99.614 420 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.16 % Allowed : 18.99 % Favored : 77.85 % 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: -0.68 (0.43), residues: 369 helix: 0.29 (0.42), residues: 155 sheet: 0.17 (0.65), residues: 60 loop : -1.43 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 78 HIS 0.005 0.001 HIS F 370 PHE 0.012 0.001 PHE F 254 TYR 0.011 0.001 TYR F 293 ARG 0.003 0.000 ARG F 195 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 138) hydrogen bonds : angle 4.75171 ( 366) SS BOND : bond 0.00084 ( 1) SS BOND : angle 1.03927 ( 2) covalent geometry : bond 0.00293 ( 3013) covalent geometry : angle 0.65013 ( 4087) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.334 Fit side-chains REVERT: F 142 TYR cc_start: 0.8452 (m-80) cc_final: 0.8243 (m-80) REVERT: F 324 MET cc_start: 0.3977 (OUTLIER) cc_final: 0.3622 (tpp) outliers start: 10 outliers final: 6 residues processed: 58 average time/residue: 0.1059 time to fit residues: 8.1011 Evaluate side-chains 50 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 256 CYS Chi-restraints excluded: chain F residue 324 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 23 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 chunk 15 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.0870 chunk 27 optimal weight: 0.7980 chunk 10 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: F 77 ASN F 100 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.132459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.117263 restraints weight = 4161.881| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.71 r_work: 0.3240 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3014 Z= 0.121 Angle : 0.607 6.945 4089 Z= 0.299 Chirality : 0.044 0.145 453 Planarity : 0.004 0.038 523 Dihedral : 7.526 92.464 420 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.38 % Allowed : 18.35 % Favored : 76.27 % 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: -0.33 (0.43), residues: 369 helix: 0.78 (0.43), residues: 150 sheet: 0.27 (0.62), residues: 65 loop : -1.43 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 78 HIS 0.004 0.001 HIS F 370 PHE 0.013 0.001 PHE F 254 TYR 0.011 0.001 TYR F 293 ARG 0.003 0.000 ARG F 195 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 138) hydrogen bonds : angle 4.39780 ( 366) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.95364 ( 2) covalent geometry : bond 0.00283 ( 3013) covalent geometry : angle 0.60722 ( 4087) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.318 Fit side-chains REVERT: F 240 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6740 (pp20) REVERT: F 324 MET cc_start: 0.4161 (OUTLIER) cc_final: 0.3807 (tpp) outliers start: 17 outliers final: 8 residues processed: 59 average time/residue: 0.1047 time to fit residues: 8.1848 Evaluate side-chains 52 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 240 GLU Chi-restraints excluded: chain F residue 256 CYS Chi-restraints excluded: chain F residue 324 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 1 optimal weight: 7.9990 chunk 30 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 0.0370 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN ** F 136 GLN ** 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 = 0.3516 r_free = 0.3516 target = 0.131551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.116205 restraints weight = 4188.368| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.78 r_work: 0.3228 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3014 Z= 0.114 Angle : 0.591 6.963 4089 Z= 0.290 Chirality : 0.043 0.140 453 Planarity : 0.004 0.036 523 Dihedral : 7.379 90.090 420 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.11 % Allowed : 19.30 % Favored : 76.58 % 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: -0.10 (0.43), residues: 369 helix: 0.93 (0.43), residues: 150 sheet: 0.44 (0.63), residues: 65 loop : -1.28 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 78 HIS 0.003 0.001 HIS F 370 PHE 0.013 0.001 PHE F 254 TYR 0.010 0.001 TYR F 293 ARG 0.003 0.000 ARG F 195 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 138) hydrogen bonds : angle 4.34191 ( 366) SS BOND : bond 0.00085 ( 1) SS BOND : angle 0.94855 ( 2) covalent geometry : bond 0.00264 ( 3013) covalent geometry : angle 0.59090 ( 4087) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.352 Fit side-chains REVERT: F 240 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6733 (pp20) REVERT: F 282 MET cc_start: 0.8384 (mmm) cc_final: 0.8142 (mmm) outliers start: 13 outliers final: 9 residues processed: 50 average time/residue: 0.1226 time to fit residues: 8.1825 Evaluate side-chains 52 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 142 TYR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 240 GLU Chi-restraints excluded: chain F residue 256 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 12 optimal weight: 0.0030 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN ** F 136 GLN ** 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 = 0.3464 r_free = 0.3464 target = 0.127808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.113892 restraints weight = 4348.011| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.69 r_work: 0.3195 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3014 Z= 0.127 Angle : 0.598 6.973 4089 Z= 0.292 Chirality : 0.044 0.140 453 Planarity : 0.004 0.035 523 Dihedral : 7.355 90.146 420 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.75 % Allowed : 18.67 % Favored : 76.58 % 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: 0.19 (0.44), residues: 369 helix: 1.13 (0.44), residues: 143 sheet: 0.78 (0.66), residues: 60 loop : -1.03 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 78 HIS 0.003 0.001 HIS F 100 PHE 0.014 0.001 PHE F 254 TYR 0.010 0.001 TYR F 293 ARG 0.002 0.000 ARG F 255 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 138) hydrogen bonds : angle 4.31915 ( 366) SS BOND : bond 0.00106 ( 1) SS BOND : angle 1.06320 ( 2) covalent geometry : bond 0.00301 ( 3013) covalent geometry : angle 0.59742 ( 4087) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.364 Fit side-chains REVERT: F 240 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6752 (pp20) REVERT: F 282 MET cc_start: 0.8370 (mmm) cc_final: 0.8143 (mmm) REVERT: F 324 MET cc_start: 0.3987 (OUTLIER) cc_final: 0.3656 (tpp) REVERT: F 345 LEU cc_start: 0.8982 (tp) cc_final: 0.8758 (tt) outliers start: 15 outliers final: 10 residues processed: 52 average time/residue: 0.0902 time to fit residues: 6.5440 Evaluate side-chains 53 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 142 TYR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 240 GLU Chi-restraints excluded: chain F residue 256 CYS Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 324 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN ** F 136 GLN ** 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 = 0.3432 r_free = 0.3432 target = 0.125113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.111002 restraints weight = 4365.809| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.75 r_work: 0.3163 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3014 Z= 0.168 Angle : 0.624 6.966 4089 Z= 0.309 Chirality : 0.045 0.147 453 Planarity : 0.004 0.037 523 Dihedral : 7.506 93.604 420 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.06 % Allowed : 18.67 % Favored : 76.27 % 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: 0.07 (0.43), residues: 369 helix: 0.98 (0.44), residues: 143 sheet: 0.78 (0.66), residues: 60 loop : -1.06 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 78 HIS 0.004 0.001 HIS F 100 PHE 0.014 0.001 PHE F 254 TYR 0.011 0.001 TYR F 293 ARG 0.002 0.000 ARG F 255 Details of bonding type rmsd hydrogen bonds : bond 0.03662 ( 138) hydrogen bonds : angle 4.36807 ( 366) SS BOND : bond 0.00227 ( 1) SS BOND : angle 1.42424 ( 2) covalent geometry : bond 0.00407 ( 3013) covalent geometry : angle 0.62304 ( 4087) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.353 Fit side-chains REVERT: F 7 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8394 (mt) REVERT: F 240 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6852 (pp20) REVERT: F 282 MET cc_start: 0.8351 (mmm) cc_final: 0.8083 (mmm) outliers start: 16 outliers final: 9 residues processed: 54 average time/residue: 0.1089 time to fit residues: 7.8216 Evaluate side-chains 55 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 240 GLU Chi-restraints excluded: chain F residue 256 CYS Chi-restraints excluded: chain F residue 303 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN ** F 136 GLN ** 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 = 0.3438 r_free = 0.3438 target = 0.125611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111668 restraints weight = 4316.824| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.73 r_work: 0.3175 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3014 Z= 0.135 Angle : 0.606 6.885 4089 Z= 0.299 Chirality : 0.044 0.142 453 Planarity : 0.004 0.035 523 Dihedral : 7.479 94.209 420 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.75 % Allowed : 19.30 % Favored : 75.95 % 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: 0.14 (0.43), residues: 369 helix: 1.05 (0.44), residues: 143 sheet: 0.78 (0.65), residues: 60 loop : -1.00 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 78 HIS 0.003 0.001 HIS F 100 PHE 0.013 0.001 PHE F 254 TYR 0.007 0.001 TYR F 293 ARG 0.002 0.000 ARG F 255 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 138) hydrogen bonds : angle 4.31551 ( 366) SS BOND : bond 0.00165 ( 1) SS BOND : angle 1.12090 ( 2) covalent geometry : bond 0.00323 ( 3013) covalent geometry : angle 0.60538 ( 4087) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.355 Fit side-chains REVERT: F 7 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8379 (mt) REVERT: F 240 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6809 (pp20) REVERT: F 282 MET cc_start: 0.8320 (mmm) cc_final: 0.8054 (mmm) REVERT: F 354 MET cc_start: 0.7940 (mpp) cc_final: 0.7384 (mpp) outliers start: 15 outliers final: 10 residues processed: 56 average time/residue: 0.1366 time to fit residues: 9.9745 Evaluate side-chains 54 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 142 TYR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 240 GLU Chi-restraints excluded: chain F residue 256 CYS Chi-restraints excluded: chain F residue 303 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.125446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111622 restraints weight = 4284.916| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.72 r_work: 0.3167 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3014 Z= 0.142 Angle : 0.624 6.883 4089 Z= 0.305 Chirality : 0.045 0.167 453 Planarity : 0.004 0.036 523 Dihedral : 7.495 94.953 420 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.11 % Allowed : 19.94 % Favored : 75.95 % 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: 0.18 (0.43), residues: 369 helix: 1.10 (0.44), residues: 143 sheet: 0.84 (0.65), residues: 60 loop : -1.03 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 78 HIS 0.003 0.001 HIS F 100 PHE 0.013 0.001 PHE F 254 TYR 0.008 0.001 TYR F 293 ARG 0.002 0.000 ARG F 255 Details of bonding type rmsd hydrogen bonds : bond 0.03372 ( 138) hydrogen bonds : angle 4.30913 ( 366) SS BOND : bond 0.00171 ( 1) SS BOND : angle 1.17021 ( 2) covalent geometry : bond 0.00341 ( 3013) covalent geometry : angle 0.62373 ( 4087) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.308 Fit side-chains REVERT: F 7 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8388 (mt) REVERT: F 240 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6826 (pp20) REVERT: F 282 MET cc_start: 0.8300 (mmm) cc_final: 0.8042 (mmm) REVERT: F 354 MET cc_start: 0.7977 (mpp) cc_final: 0.7391 (mpp) outliers start: 13 outliers final: 9 residues processed: 51 average time/residue: 0.1178 time to fit residues: 8.0344 Evaluate side-chains 52 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 142 TYR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 240 GLU Chi-restraints excluded: chain F residue 256 CYS Chi-restraints excluded: chain F residue 303 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 9 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.128469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.114331 restraints weight = 4281.638| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.78 r_work: 0.3208 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3014 Z= 0.111 Angle : 0.608 8.435 4089 Z= 0.292 Chirality : 0.043 0.131 453 Planarity : 0.004 0.033 523 Dihedral : 7.270 91.023 420 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.16 % Allowed : 21.20 % Favored : 75.63 % 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: 0.40 (0.44), residues: 369 helix: 1.31 (0.45), residues: 143 sheet: 0.90 (0.65), residues: 60 loop : -0.91 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 78 HIS 0.002 0.001 HIS F 100 PHE 0.013 0.001 PHE F 254 TYR 0.007 0.001 TYR F 293 ARG 0.001 0.000 ARG F 205 Details of bonding type rmsd hydrogen bonds : bond 0.02814 ( 138) hydrogen bonds : angle 4.20634 ( 366) SS BOND : bond 0.00073 ( 1) SS BOND : angle 0.75826 ( 2) covalent geometry : bond 0.00257 ( 3013) covalent geometry : angle 0.60791 ( 4087) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 738 Ramachandran restraints generated. 369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.338 Fit side-chains REVERT: F 7 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8362 (mt) REVERT: F 52 TYR cc_start: 0.8798 (m-80) cc_final: 0.8589 (m-80) REVERT: F 240 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6768 (pp20) REVERT: F 282 MET cc_start: 0.8209 (mmm) cc_final: 0.7967 (mmm) REVERT: F 354 MET cc_start: 0.7942 (mpp) cc_final: 0.7395 (mpp) REVERT: F 370 HIS cc_start: 0.8484 (m-70) cc_final: 0.8268 (m90) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 0.1218 time to fit residues: 8.4743 Evaluate side-chains 54 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 142 TYR Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 240 GLU Chi-restraints excluded: chain F residue 256 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110455 restraints weight = 4244.751| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.78 r_work: 0.3165 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3014 Z= 0.173 Angle : 0.664 9.027 4089 Z= 0.322 Chirality : 0.046 0.154 453 Planarity : 0.004 0.037 523 Dihedral : 7.499 95.761 420 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.48 % Allowed : 20.57 % Favored : 75.95 % 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: 0.15 (0.44), residues: 369 helix: 1.08 (0.44), residues: 143 sheet: 0.86 (0.65), residues: 60 loop : -1.07 (0.48), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 78 HIS 0.004 0.001 HIS F 100 PHE 0.015 0.002 PHE F 254 TYR 0.012 0.001 TYR F 293 ARG 0.002 0.000 ARG F 255 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 138) hydrogen bonds : angle 4.27928 ( 366) SS BOND : bond 0.00243 ( 1) SS BOND : angle 1.47886 ( 2) covalent geometry : bond 0.00419 ( 3013) covalent geometry : angle 0.66381 ( 4087) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1900.62 seconds wall clock time: 33 minutes 12.47 seconds (1992.47 seconds total)