Starting phenix.real_space_refine on Fri Aug 22 13:06:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cog_16776/08_2025/8cog_16776.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cog_16776/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8cog_16776/08_2025/8cog_16776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cog_16776/08_2025/8cog_16776.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cog_16776/08_2025/8cog_16776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cog_16776/08_2025/8cog_16776.map" } resolution = 3.499 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 0.71, per 1000 atoms: 0.24 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: 0.23 Conformation dependent library (CDL) restraints added in 70.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.10 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: 0.35 Time building geometry restraints manager: 0.28 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: 1.050 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.980 Find NCS groups from input model: 0.010 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.100 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.025 0.003 ARG F 311 TYR 0.041 0.009 TYR F 68 PHE 0.042 0.010 PHE F 30 TRP 0.044 0.012 TRP F 78 HIS 0.010 0.004 HIS F 86 Details of bonding type rmsd covalent geometry : bond 0.01700 ( 3013) covalent geometry : angle 2.04416 ( 4087) SS BOND : bond 0.06635 ( 1) SS BOND : angle 5.79690 ( 2) hydrogen bonds : bond 0.27929 ( 138) hydrogen bonds : angle 9.74922 ( 366) *********************** 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 : 0.124 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: 0.8707 (p0) REVERT: F 40 GLN cc_start: 0.7500 (mt0) cc_final: 0.7162 (pm20) REVERT: F 182 ARG cc_start: 0.8514 (ttp80) cc_final: 0.8285 (tpp80) REVERT: F 240 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7352 (pp20) REVERT: F 313 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7474 (tp40) outliers start: 7 outliers final: 0 residues processed: 89 average time/residue: 0.0677 time to fit residues: 7.0677 Evaluate side-chains 54 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 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 F 352 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115889 restraints weight = 4136.957| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.82 r_work: 0.3229 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3014 Z= 0.175 Angle : 0.723 7.841 4089 Z= 0.368 Chirality : 0.049 0.287 453 Planarity : 0.005 0.039 523 Dihedral : 8.528 113.767 420 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.85 % Allowed : 17.41 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.41), residues: 369 helix: -0.33 (0.40), residues: 155 sheet: 0.09 (0.73), residues: 45 loop : -1.75 (0.45), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 195 TYR 0.017 0.002 TYR F 293 PHE 0.013 0.002 PHE F 261 TRP 0.011 0.002 TRP F 85 HIS 0.006 0.002 HIS F 370 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 3013) covalent geometry : angle 0.72279 ( 4087) SS BOND : bond 0.00334 ( 1) SS BOND : angle 1.42259 ( 2) hydrogen bonds : bond 0.04753 ( 138) hydrogen bonds : angle 5.29238 ( 366) *********************** 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 71 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.072 Fit side-chains REVERT: F 4 ILE cc_start: 0.8205 (pt) cc_final: 0.7869 (mt) REVERT: F 136 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8342 (mm-40) REVERT: F 142 TYR cc_start: 0.8563 (m-80) cc_final: 0.8317 (m-80) REVERT: F 324 MET cc_start: 0.3631 (OUTLIER) cc_final: 0.3313 (tpp) outliers start: 9 outliers final: 5 residues processed: 67 average time/residue: 0.0562 time to fit residues: 4.7292 Evaluate side-chains 55 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 17 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 5 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 100 HIS F 110 ASN F 136 GLN ** F 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.129916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.114549 restraints weight = 4202.831| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.77 r_work: 0.3204 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3014 Z= 0.146 Angle : 0.663 8.222 4089 Z= 0.329 Chirality : 0.045 0.151 453 Planarity : 0.004 0.040 523 Dihedral : 7.850 100.215 420 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.75 % Allowed : 18.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.42), residues: 369 helix: 0.37 (0.42), residues: 149 sheet: -0.25 (0.61), residues: 67 loop : -1.64 (0.47), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 195 TYR 0.012 0.001 TYR F 293 PHE 0.012 0.001 PHE F 254 TRP 0.014 0.002 TRP F 78 HIS 0.005 0.001 HIS F 370 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 3013) covalent geometry : angle 0.66236 ( 4087) SS BOND : bond 0.00160 ( 1) SS BOND : angle 1.24591 ( 2) hydrogen bonds : bond 0.04132 ( 138) hydrogen bonds : angle 4.78588 ( 366) *********************** 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 68 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.116 Fit side-chains REVERT: F 142 TYR cc_start: 0.8484 (m-80) cc_final: 0.8278 (m-80) REVERT: F 324 MET cc_start: 0.4056 (OUTLIER) cc_final: 0.3708 (tpp) outliers start: 15 outliers final: 9 residues processed: 61 average time/residue: 0.0554 time to fit residues: 4.2921 Evaluate side-chains 55 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain F residue 369 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.130863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.115345 restraints weight = 4161.287| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.80 r_work: 0.3216 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3014 Z= 0.127 Angle : 0.612 6.917 4089 Z= 0.307 Chirality : 0.044 0.164 453 Planarity : 0.004 0.035 523 Dihedral : 7.586 94.352 420 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.06 % Allowed : 17.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.43), residues: 369 helix: 0.70 (0.43), residues: 149 sheet: 0.23 (0.61), residues: 65 loop : -1.53 (0.47), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 195 TYR 0.011 0.001 TYR F 293 PHE 0.013 0.001 PHE F 254 TRP 0.011 0.001 TRP F 78 HIS 0.004 0.001 HIS F 370 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3013) covalent geometry : angle 0.61222 ( 4087) SS BOND : bond 0.00087 ( 1) SS BOND : angle 0.96643 ( 2) hydrogen bonds : bond 0.03418 ( 138) hydrogen bonds : angle 4.45976 ( 366) *********************** 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 64 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.120 Fit side-chains REVERT: F 324 MET cc_start: 0.4083 (OUTLIER) cc_final: 0.3715 (tpp) outliers start: 16 outliers final: 8 residues processed: 58 average time/residue: 0.0559 time to fit residues: 4.1343 Evaluate side-chains 50 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 11 ASN F 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116742 restraints weight = 4159.874| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.68 r_work: 0.3240 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3014 Z= 0.123 Angle : 0.602 6.918 4089 Z= 0.297 Chirality : 0.044 0.143 453 Planarity : 0.004 0.033 523 Dihedral : 7.411 91.316 420 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.06 % Allowed : 17.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.43), residues: 369 helix: 0.82 (0.43), residues: 150 sheet: 0.61 (0.65), residues: 60 loop : -1.37 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 195 TYR 0.011 0.001 TYR F 293 PHE 0.014 0.001 PHE F 254 TRP 0.010 0.001 TRP F 78 HIS 0.003 0.001 HIS F 100 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3013) covalent geometry : angle 0.60116 ( 4087) SS BOND : bond 0.00144 ( 1) SS BOND : angle 1.10822 ( 2) hydrogen bonds : bond 0.03269 ( 138) hydrogen bonds : angle 4.33767 ( 366) *********************** 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 63 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.118 Fit side-chains REVERT: F 282 MET cc_start: 0.8365 (mmm) cc_final: 0.8106 (mmm) REVERT: F 324 MET cc_start: 0.3786 (OUTLIER) cc_final: 0.3569 (tpp) outliers start: 16 outliers final: 11 residues processed: 57 average time/residue: 0.0588 time to fit residues: 4.2603 Evaluate side-chains 56 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain F residue 324 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 0.0770 chunk 26 optimal weight: 0.1980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.114273 restraints weight = 4217.623| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.67 r_work: 0.3202 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4353 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= 0.122 Angle : 0.594 6.946 4089 Z= 0.293 Chirality : 0.044 0.141 453 Planarity : 0.004 0.032 523 Dihedral : 7.381 90.725 420 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.75 % Allowed : 18.04 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.43), residues: 369 helix: 1.11 (0.44), residues: 143 sheet: 0.70 (0.66), residues: 60 loop : -1.08 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 255 TYR 0.010 0.001 TYR F 293 PHE 0.013 0.001 PHE F 254 TRP 0.008 0.001 TRP F 78 HIS 0.003 0.001 HIS F 100 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 3013) covalent geometry : angle 0.59377 ( 4087) SS BOND : bond 0.00101 ( 1) SS BOND : angle 0.99443 ( 2) hydrogen bonds : bond 0.03140 ( 138) hydrogen bonds : angle 4.29493 ( 366) *********************** 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 60 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.125 Fit side-chains REVERT: F 7 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8380 (mt) REVERT: F 282 MET cc_start: 0.8333 (mmm) cc_final: 0.8066 (mmm) REVERT: F 345 LEU cc_start: 0.9025 (tp) cc_final: 0.8807 (tt) outliers start: 15 outliers final: 12 residues processed: 55 average time/residue: 0.0447 time to fit residues: 3.3035 Evaluate side-chains 59 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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 70 ILE Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 122 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 1 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 30 optimal weight: 0.4980 chunk 3 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113392 restraints weight = 4300.909| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.81 r_work: 0.3194 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4466 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= 0.119 Angle : 0.586 6.951 4089 Z= 0.289 Chirality : 0.043 0.140 453 Planarity : 0.004 0.030 523 Dihedral : 7.332 89.894 420 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.43), residues: 369 helix: 1.17 (0.44), residues: 143 sheet: 0.74 (0.66), residues: 60 loop : -0.97 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 255 TYR 0.010 0.001 TYR F 293 PHE 0.013 0.001 PHE F 254 TRP 0.009 0.001 TRP F 78 HIS 0.003 0.001 HIS F 100 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3013) covalent geometry : angle 0.58576 ( 4087) SS BOND : bond 0.00116 ( 1) SS BOND : angle 0.95566 ( 2) hydrogen bonds : bond 0.03080 ( 138) hydrogen bonds : angle 4.23779 ( 366) *********************** 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 62 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.070 Fit side-chains REVERT: F 7 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8373 (mt) REVERT: F 240 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6781 (pp20) REVERT: F 282 MET cc_start: 0.8323 (mmm) cc_final: 0.8075 (mmm) REVERT: F 345 LEU cc_start: 0.9035 (tp) cc_final: 0.8802 (tt) outliers start: 15 outliers final: 10 residues processed: 56 average time/residue: 0.0471 time to fit residues: 3.4420 Evaluate side-chains 55 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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 70 ILE Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 122 MET 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 11 optimal weight: 0.0670 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.127104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112762 restraints weight = 4344.690| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.82 r_work: 0.3189 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4534 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 : 0.593 6.954 4089 Z= 0.293 Chirality : 0.044 0.141 453 Planarity : 0.004 0.030 523 Dihedral : 7.332 90.114 420 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.43 % Allowed : 19.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.43), residues: 369 helix: 1.18 (0.44), residues: 143 sheet: 0.76 (0.66), residues: 60 loop : -0.90 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 255 TYR 0.005 0.001 TYR F 293 PHE 0.013 0.001 PHE F 254 TRP 0.009 0.001 TRP F 78 HIS 0.003 0.001 HIS F 100 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3013) covalent geometry : angle 0.59289 ( 4087) SS BOND : bond 0.00121 ( 1) SS BOND : angle 1.03986 ( 2) hydrogen bonds : bond 0.03137 ( 138) hydrogen bonds : angle 4.22531 ( 366) *********************** 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 59 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.124 Fit side-chains REVERT: F 7 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8408 (mt) REVERT: F 240 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6835 (pp20) REVERT: F 282 MET cc_start: 0.8295 (mmm) cc_final: 0.8039 (mmm) outliers start: 14 outliers final: 11 residues processed: 54 average time/residue: 0.0486 time to fit residues: 3.4615 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 : 0.114 ------------------------------------------------------------------------------- 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 70 ILE Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 122 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 11 optimal weight: 0.0870 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.127197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113291 restraints weight = 4308.021| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.71 r_work: 0.3198 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3014 Z= 0.123 Angle : 0.591 6.949 4089 Z= 0.291 Chirality : 0.043 0.139 453 Planarity : 0.004 0.030 523 Dihedral : 7.322 90.179 420 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.43 % Allowed : 18.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.43), residues: 369 helix: 1.22 (0.44), residues: 143 sheet: 0.81 (0.65), residues: 60 loop : -0.87 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 255 TYR 0.007 0.001 TYR F 293 PHE 0.013 0.001 PHE F 254 TRP 0.008 0.001 TRP F 78 HIS 0.003 0.001 HIS F 100 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3013) covalent geometry : angle 0.59040 ( 4087) SS BOND : bond 0.00115 ( 1) SS BOND : angle 0.99748 ( 2) hydrogen bonds : bond 0.03060 ( 138) hydrogen bonds : angle 4.21462 ( 366) *********************** 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 58 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.137 Fit side-chains REVERT: F 7 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8396 (mt) REVERT: F 240 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6849 (pp20) REVERT: F 282 MET cc_start: 0.8256 (mmm) cc_final: 0.8011 (mmm) outliers start: 14 outliers final: 11 residues processed: 53 average time/residue: 0.0516 time to fit residues: 3.5281 Evaluate side-chains 56 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.074 ------------------------------------------------------------------------------- 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 70 ILE Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 122 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 6 optimal weight: 0.2980 chunk 11 optimal weight: 0.0040 chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113664 restraints weight = 4267.637| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.71 r_work: 0.3203 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3014 Z= 0.121 Angle : 0.605 6.953 4089 Z= 0.293 Chirality : 0.044 0.161 453 Planarity : 0.004 0.029 523 Dihedral : 7.302 90.092 420 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.43), residues: 369 helix: 1.27 (0.44), residues: 143 sheet: 0.84 (0.65), residues: 60 loop : -0.86 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 255 TYR 0.012 0.001 TYR F 293 PHE 0.013 0.001 PHE F 254 TRP 0.009 0.001 TRP F 78 HIS 0.003 0.001 HIS F 100 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 3013) covalent geometry : angle 0.60460 ( 4087) SS BOND : bond 0.00124 ( 1) SS BOND : angle 0.97068 ( 2) hydrogen bonds : bond 0.03003 ( 138) hydrogen bonds : angle 4.18978 ( 366) ********************** 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: 13 poor density : 46 time to evaluate : 0.070 Fit side-chains REVERT: F 7 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8346 (mt) REVERT: F 240 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6835 (pp20) REVERT: F 282 MET cc_start: 0.8230 (mmm) cc_final: 0.7986 (mmm) REVERT: F 354 MET cc_start: 0.7928 (mmm) cc_final: 0.7652 (mpp) outliers start: 13 outliers final: 10 residues processed: 54 average time/residue: 0.0419 time to fit residues: 3.0200 Evaluate side-chains 55 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112781 restraints weight = 4283.527| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.70 r_work: 0.3197 rms_B_bonded: 2.10 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: 0.8124 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3014 Z= 0.136 Angle : 0.617 6.911 4089 Z= 0.300 Chirality : 0.044 0.169 453 Planarity : 0.004 0.031 523 Dihedral : 7.356 91.171 420 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.11 % Allowed : 18.99 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.43), residues: 369 helix: 1.26 (0.44), residues: 143 sheet: 0.89 (0.64), residues: 60 loop : -0.97 (0.47), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 255 TYR 0.013 0.001 TYR F 293 PHE 0.013 0.001 PHE F 254 TRP 0.008 0.001 TRP F 78 HIS 0.003 0.001 HIS F 100 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3013) covalent geometry : angle 0.61673 ( 4087) SS BOND : bond 0.00154 ( 1) SS BOND : angle 1.11103 ( 2) hydrogen bonds : bond 0.03153 ( 138) hydrogen bonds : angle 4.21635 ( 366) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 935.22 seconds wall clock time: 16 minutes 47.38 seconds (1007.38 seconds total)