Starting phenix.real_space_refine on Fri May 9 13:49:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iwe_35765/05_2025/8iwe_35765_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iwe_35765/05_2025/8iwe_35765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iwe_35765/05_2025/8iwe_35765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iwe_35765/05_2025/8iwe_35765.map" model { file = "/net/cci-nas-00/data/ceres_data/8iwe_35765/05_2025/8iwe_35765_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iwe_35765/05_2025/8iwe_35765_neut.cif" } resolution = 3.4 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 1497 2.51 5 N 353 2.21 5 O 374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 2236 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2226 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 12, 'TRANS': 283} Chain breaks: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'SPD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.03, per 1000 atoms: 0.91 Number of scatterers: 2236 At special positions: 0 Unit cell: (63.403, 75.905, 75.012, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 374 8.00 N 353 7.00 C 1497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 190 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 271.2 milliseconds 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 562 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 0 sheets defined 78.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'R' and resid 35 through 57 removed outlier: 4.975A pdb=" N LEU R 41 " --> pdb=" O GLY R 37 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA R 43 " --> pdb=" O LEU R 39 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL R 53 " --> pdb=" O GLY R 49 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE R 55 " --> pdb=" O LEU R 51 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA R 56 " --> pdb=" O LEU R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 85 removed outlier: 4.114A pdb=" N VAL R 71 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL R 81 " --> pdb=" O ALA R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 96 Processing helix chain 'R' and resid 104 through 136 removed outlier: 3.657A pdb=" N THR R 109 " --> pdb=" O CYS R 105 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS R 110 " --> pdb=" O LYS R 106 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP R 112 " --> pdb=" O HIS R 108 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR R 113 " --> pdb=" O THR R 109 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER R 114 " --> pdb=" O CYS R 110 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE R 117 " --> pdb=" O THR R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 144 removed outlier: 3.735A pdb=" N LYS R 143 " --> pdb=" O THR R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 169 removed outlier: 3.776A pdb=" N PHE R 158 " --> pdb=" O ALA R 154 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER R 164 " --> pdb=" O SER R 160 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER R 166 " --> pdb=" O THR R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 232 removed outlier: 4.340A pdb=" N LEU R 200 " --> pdb=" O GLN R 196 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU R 201 " --> pdb=" O ASN R 197 " (cutoff:3.500A) Proline residue: R 209 - end of helix removed outlier: 3.991A pdb=" N VAL R 212 " --> pdb=" O LEU R 208 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 283 removed outlier: 4.395A pdb=" N LYS R 251 " --> pdb=" O GLU R 247 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG R 252 " --> pdb=" O ARG R 248 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR R 259 " --> pdb=" O LYS R 255 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU R 260 " --> pdb=" O ALA R 256 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA R 263 " --> pdb=" O THR R 259 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER R 270 " --> pdb=" O ALA R 266 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 3.772A pdb=" N ALA R 282 " --> pdb=" O ALA R 278 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR R 283 " --> pdb=" O VAL R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 312 removed outlier: 3.610A pdb=" N TYR R 293 " --> pdb=" O PRO R 289 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL R 300 " --> pdb=" O LEU R 296 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN R 303 " --> pdb=" O CYS R 299 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER R 304 " --> pdb=" O VAL R 300 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA R 305 " --> pdb=" O TYR R 301 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 315 through 327 144 hydrogen bonds defined for protein. 432 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: 0.51 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 346 1.32 - 1.45: 686 1.45 - 1.57: 1255 1.57 - 1.69: 0 1.69 - 1.81: 15 Bond restraints: 2302 Sorted by residual: bond pdb=" C VAL R 94 " pdb=" O VAL R 94 " ideal model delta sigma weight residual 1.236 1.202 0.034 1.23e-02 6.61e+03 7.83e+00 bond pdb=" CA VAL R 94 " pdb=" CB VAL R 94 " ideal model delta sigma weight residual 1.540 1.510 0.030 1.37e-02 5.33e+03 4.72e+00 bond pdb=" CA ILE R 280 " pdb=" C ILE R 280 " ideal model delta sigma weight residual 1.519 1.542 -0.023 1.14e-02 7.69e+03 4.22e+00 bond pdb=" CA VAL R 94 " pdb=" C VAL R 94 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.39e-02 5.18e+03 3.44e+00 bond pdb=" CA TYR R 302 " pdb=" C TYR R 302 " ideal model delta sigma weight residual 1.522 1.498 0.024 1.41e-02 5.03e+03 2.94e+00 ... (remaining 2297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 2999 1.92 - 3.85: 119 3.85 - 5.77: 19 5.77 - 7.70: 8 7.70 - 9.62: 3 Bond angle restraints: 3148 Sorted by residual: angle pdb=" N ASN R 303 " pdb=" CA ASN R 303 " pdb=" C ASN R 303 " ideal model delta sigma weight residual 112.38 103.43 8.95 1.22e+00 6.72e-01 5.38e+01 angle pdb=" N ILE R 280 " pdb=" CA ILE R 280 " pdb=" C ILE R 280 " ideal model delta sigma weight residual 113.07 122.36 -9.29 1.36e+00 5.41e-01 4.66e+01 angle pdb=" C TYR R 315 " pdb=" N PRO R 316 " pdb=" CA PRO R 316 " ideal model delta sigma weight residual 119.84 126.85 -7.01 1.25e+00 6.40e-01 3.15e+01 angle pdb=" N PHE R 286 " pdb=" CA PHE R 286 " pdb=" C PHE R 286 " ideal model delta sigma weight residual 111.54 119.15 -7.61 1.36e+00 5.41e-01 3.13e+01 angle pdb=" N PHE R 207 " pdb=" CA PHE R 207 " pdb=" C PHE R 207 " ideal model delta sigma weight residual 111.36 116.49 -5.13 1.09e+00 8.42e-01 2.21e+01 ... (remaining 3143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.82: 1053 11.82 - 23.64: 149 23.64 - 35.45: 63 35.45 - 47.27: 30 47.27 - 59.09: 11 Dihedral angle restraints: 1306 sinusoidal: 434 harmonic: 872 Sorted by residual: dihedral pdb=" C VAL R 279 " pdb=" N VAL R 279 " pdb=" CA VAL R 279 " pdb=" CB VAL R 279 " ideal model delta harmonic sigma weight residual -122.00 -137.52 15.52 0 2.50e+00 1.60e-01 3.85e+01 dihedral pdb=" N VAL R 279 " pdb=" C VAL R 279 " pdb=" CA VAL R 279 " pdb=" CB VAL R 279 " ideal model delta harmonic sigma weight residual 123.40 133.59 -10.19 0 2.50e+00 1.60e-01 1.66e+01 dihedral pdb=" N TRP R 317 " pdb=" C TRP R 317 " pdb=" CA TRP R 317 " pdb=" CB TRP R 317 " ideal model delta harmonic sigma weight residual 122.80 130.73 -7.93 0 2.50e+00 1.60e-01 1.01e+01 ... (remaining 1303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 334 0.090 - 0.180: 22 0.180 - 0.269: 6 0.269 - 0.359: 2 0.359 - 0.449: 2 Chirality restraints: 366 Sorted by residual: chirality pdb=" CA VAL R 279 " pdb=" N VAL R 279 " pdb=" C VAL R 279 " pdb=" CB VAL R 279 " both_signs ideal model delta sigma weight residual False 2.44 1.99 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CA PHE R 286 " pdb=" N PHE R 286 " pdb=" C PHE R 286 " pdb=" CB PHE R 286 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA TRP R 317 " pdb=" N TRP R 317 " pdb=" C TRP R 317 " pdb=" CB TRP R 317 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 ... (remaining 363 not shown) Planarity restraints: 385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 301 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.25e+00 pdb=" C TYR R 301 " 0.053 2.00e-02 2.50e+03 pdb=" O TYR R 301 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR R 302 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 147 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C SER R 147 " -0.036 2.00e-02 2.50e+03 pdb=" O SER R 147 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL R 148 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 95 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C GLU R 95 " 0.033 2.00e-02 2.50e+03 pdb=" O GLU R 95 " -0.012 2.00e-02 2.50e+03 pdb=" N SER R 96 " -0.011 2.00e-02 2.50e+03 ... (remaining 382 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 798 2.84 - 3.35: 2124 3.35 - 3.87: 3444 3.87 - 4.38: 3753 4.38 - 4.90: 6479 Nonbonded interactions: 16598 Sorted by model distance: nonbonded pdb=" OD2 ASP R 112 " pdb=" OH TYR R 301 " model vdw 2.321 3.040 nonbonded pdb=" OD2 ASP R 281 " pdb=" OG1 THR R 288 " model vdw 2.386 3.040 nonbonded pdb=" O THR R 109 " pdb=" OG1 THR R 113 " model vdw 2.422 3.040 nonbonded pdb=" O ASP R 281 " pdb=" O MET R 284 " model vdw 2.450 3.040 nonbonded pdb=" O THR R 139 " pdb=" OG1 THR R 139 " model vdw 2.472 3.040 ... (remaining 16593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.270 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 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 : 0.004 0.034 2304 Z= 0.266 Angle : 0.934 9.620 3152 Z= 0.640 Chirality : 0.067 0.449 366 Planarity : 0.004 0.030 385 Dihedral : 16.003 59.087 738 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.84 % Allowed : 19.43 % Favored : 77.73 % Cbeta Deviations : 0.36 % 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: -0.50 (0.52), residues: 290 helix: 0.67 (0.41), residues: 196 sheet: None (None), residues: 0 loop : -2.51 (0.60), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 317 HIS 0.001 0.000 HIS R 122 PHE 0.006 0.001 PHE R 286 TYR 0.011 0.001 TYR R 99 ARG 0.002 0.000 ARG R 219 Details of bonding type rmsd hydrogen bonds : bond 0.17853 ( 144) hydrogen bonds : angle 6.38489 ( 432) SS BOND : bond 0.00555 ( 2) SS BOND : angle 0.45781 ( 4) covalent geometry : bond 0.00388 ( 2302) covalent geometry : angle 0.93489 ( 3148) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.261 Fit side-chains REVERT: R 255 LYS cc_start: 0.8616 (ttpp) cc_final: 0.8416 (tttm) outliers start: 6 outliers final: 3 residues processed: 30 average time/residue: 0.1923 time to fit residues: 6.6864 Evaluate side-chains 22 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 186 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.0770 chunk 26 optimal weight: 0.6980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 50 ASN ** 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 = 0.3395 r_free = 0.3395 target = 0.107627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.094166 restraints weight = 3944.601| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.13 r_work: 0.3109 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2304 Z= 0.114 Angle : 0.519 5.314 3152 Z= 0.273 Chirality : 0.039 0.123 366 Planarity : 0.003 0.027 385 Dihedral : 6.791 58.992 328 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.84 % Allowed : 20.38 % Favored : 76.78 % 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: 0.48 (0.54), residues: 290 helix: 1.27 (0.40), residues: 210 sheet: None (None), residues: 0 loop : -2.29 (0.64), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 317 HIS 0.001 0.000 HIS R 59 PHE 0.007 0.001 PHE R 206 TYR 0.016 0.001 TYR R 274 ARG 0.003 0.000 ARG R 219 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 144) hydrogen bonds : angle 4.21755 ( 432) SS BOND : bond 0.00144 ( 2) SS BOND : angle 0.79071 ( 4) covalent geometry : bond 0.00237 ( 2302) covalent geometry : angle 0.51819 ( 3148) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.228 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 29 average time/residue: 0.1777 time to fit residues: 6.0276 Evaluate side-chains 23 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 306 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.102991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.090694 restraints weight = 4082.198| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.97 r_work: 0.3091 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2304 Z= 0.127 Angle : 0.515 5.474 3152 Z= 0.269 Chirality : 0.039 0.112 366 Planarity : 0.004 0.038 385 Dihedral : 6.047 55.941 325 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.27 % Allowed : 21.33 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.55), residues: 290 helix: 1.43 (0.41), residues: 212 sheet: None (None), residues: 0 loop : -2.46 (0.66), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 317 HIS 0.001 0.000 HIS R 59 PHE 0.007 0.001 PHE R 100 TYR 0.010 0.001 TYR R 283 ARG 0.004 0.000 ARG R 219 Details of bonding type rmsd hydrogen bonds : bond 0.04332 ( 144) hydrogen bonds : angle 4.02380 ( 432) SS BOND : bond 0.00210 ( 2) SS BOND : angle 1.02338 ( 4) covalent geometry : bond 0.00281 ( 2302) covalent geometry : angle 0.51420 ( 3148) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.252 Fit side-chains REVERT: R 258 LYS cc_start: 0.8241 (ttpt) cc_final: 0.7896 (ttmt) outliers start: 9 outliers final: 4 residues processed: 28 average time/residue: 0.2127 time to fit residues: 6.9327 Evaluate side-chains 25 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain R residue 326 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.105053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.092041 restraints weight = 4024.005| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.12 r_work: 0.3105 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2304 Z= 0.110 Angle : 0.500 5.486 3152 Z= 0.255 Chirality : 0.038 0.117 366 Planarity : 0.003 0.029 385 Dihedral : 4.784 45.033 324 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.32 % Allowed : 23.22 % Favored : 73.46 % 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: 0.65 (0.55), residues: 290 helix: 1.44 (0.40), residues: 212 sheet: None (None), residues: 0 loop : -2.47 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 317 HIS 0.001 0.000 HIS R 59 PHE 0.006 0.001 PHE R 206 TYR 0.008 0.001 TYR R 274 ARG 0.003 0.000 ARG R 219 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 144) hydrogen bonds : angle 3.85876 ( 432) SS BOND : bond 0.00207 ( 2) SS BOND : angle 0.98453 ( 4) covalent geometry : bond 0.00241 ( 2302) covalent geometry : angle 0.49874 ( 3148) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.242 Fit side-chains REVERT: R 258 LYS cc_start: 0.8250 (ttpt) cc_final: 0.7915 (ttmt) outliers start: 7 outliers final: 2 residues processed: 26 average time/residue: 0.2142 time to fit residues: 6.4192 Evaluate side-chains 23 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 15 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.092340 restraints weight = 4092.706| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.99 r_work: 0.3110 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2304 Z= 0.108 Angle : 0.489 5.460 3152 Z= 0.250 Chirality : 0.037 0.117 366 Planarity : 0.003 0.024 385 Dihedral : 4.847 50.975 324 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.74 % Allowed : 22.27 % Favored : 72.99 % 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: 0.73 (0.54), residues: 290 helix: 1.47 (0.39), residues: 212 sheet: None (None), residues: 0 loop : -2.38 (0.68), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 317 HIS 0.001 0.000 HIS R 59 PHE 0.006 0.001 PHE R 206 TYR 0.008 0.001 TYR R 283 ARG 0.004 0.000 ARG R 219 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 144) hydrogen bonds : angle 3.75624 ( 432) SS BOND : bond 0.00170 ( 2) SS BOND : angle 0.85028 ( 4) covalent geometry : bond 0.00237 ( 2302) covalent geometry : angle 0.48848 ( 3148) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.261 Fit side-chains REVERT: R 258 LYS cc_start: 0.8281 (ttpt) cc_final: 0.7959 (ttmt) outliers start: 10 outliers final: 5 residues processed: 31 average time/residue: 0.2331 time to fit residues: 8.1981 Evaluate side-chains 28 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 326 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 0.0170 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 0.0370 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.107551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.094384 restraints weight = 4016.193| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.15 r_work: 0.3140 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2304 Z= 0.097 Angle : 0.486 5.587 3152 Z= 0.246 Chirality : 0.037 0.118 366 Planarity : 0.003 0.022 385 Dihedral : 5.009 58.517 324 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.90 % Allowed : 24.64 % Favored : 73.46 % 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: 0.97 (0.54), residues: 290 helix: 1.64 (0.39), residues: 212 sheet: None (None), residues: 0 loop : -2.25 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 317 HIS 0.001 0.000 HIS R 59 PHE 0.005 0.000 PHE R 206 TYR 0.014 0.001 TYR R 99 ARG 0.003 0.000 ARG R 219 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 144) hydrogen bonds : angle 3.62872 ( 432) SS BOND : bond 0.00190 ( 2) SS BOND : angle 0.63265 ( 4) covalent geometry : bond 0.00210 ( 2302) covalent geometry : angle 0.48530 ( 3148) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.239 Fit side-chains REVERT: R 232 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8029 (mm-30) REVERT: R 258 LYS cc_start: 0.8229 (ttpt) cc_final: 0.7904 (ttmt) outliers start: 4 outliers final: 3 residues processed: 29 average time/residue: 0.2012 time to fit residues: 6.7475 Evaluate side-chains 27 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.106440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.093654 restraints weight = 4024.953| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.04 r_work: 0.3146 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2304 Z= 0.102 Angle : 0.495 6.037 3152 Z= 0.250 Chirality : 0.037 0.117 366 Planarity : 0.003 0.021 385 Dihedral : 5.097 59.370 324 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.37 % Allowed : 25.59 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.54), residues: 290 helix: 1.80 (0.39), residues: 212 sheet: None (None), residues: 0 loop : -2.14 (0.71), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 317 HIS 0.001 0.000 HIS R 59 PHE 0.006 0.001 PHE R 206 TYR 0.014 0.001 TYR R 99 ARG 0.004 0.000 ARG R 219 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 144) hydrogen bonds : angle 3.64967 ( 432) SS BOND : bond 0.00201 ( 2) SS BOND : angle 0.88218 ( 4) covalent geometry : bond 0.00225 ( 2302) covalent geometry : angle 0.49461 ( 3148) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.237 Fit side-chains REVERT: R 232 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8102 (mm-30) REVERT: R 258 LYS cc_start: 0.8185 (ttpt) cc_final: 0.7857 (ttmt) outliers start: 5 outliers final: 3 residues processed: 31 average time/residue: 0.2161 time to fit residues: 7.6511 Evaluate side-chains 29 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 1 optimal weight: 0.4980 chunk 7 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.107209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.094129 restraints weight = 4186.821| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.14 r_work: 0.3149 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2304 Z= 0.098 Angle : 0.482 5.463 3152 Z= 0.242 Chirality : 0.037 0.117 366 Planarity : 0.003 0.020 385 Dihedral : 5.081 59.710 324 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.37 % Allowed : 25.12 % Favored : 72.51 % 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: 1.41 (0.54), residues: 290 helix: 1.95 (0.39), residues: 212 sheet: None (None), residues: 0 loop : -2.02 (0.71), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 317 HIS 0.001 0.000 HIS R 59 PHE 0.005 0.001 PHE R 206 TYR 0.014 0.001 TYR R 99 ARG 0.004 0.000 ARG R 219 Details of bonding type rmsd hydrogen bonds : bond 0.03018 ( 144) hydrogen bonds : angle 3.60565 ( 432) SS BOND : bond 0.00199 ( 2) SS BOND : angle 1.07897 ( 4) covalent geometry : bond 0.00214 ( 2302) covalent geometry : angle 0.48102 ( 3148) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.245 Fit side-chains REVERT: R 258 LYS cc_start: 0.8153 (ttpt) cc_final: 0.7848 (ttmt) outliers start: 5 outliers final: 3 residues processed: 29 average time/residue: 0.2290 time to fit residues: 7.5517 Evaluate side-chains 29 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 269 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 25 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 0.0670 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.107035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.094209 restraints weight = 4053.257| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.05 r_work: 0.3161 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2304 Z= 0.100 Angle : 0.489 7.319 3152 Z= 0.249 Chirality : 0.037 0.117 366 Planarity : 0.003 0.020 385 Dihedral : 5.064 59.331 324 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.90 % Allowed : 25.12 % Favored : 72.99 % 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: 1.54 (0.54), residues: 290 helix: 2.03 (0.39), residues: 212 sheet: None (None), residues: 0 loop : -1.95 (0.73), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 317 HIS 0.001 0.000 HIS R 59 PHE 0.006 0.001 PHE R 206 TYR 0.014 0.001 TYR R 99 ARG 0.004 0.000 ARG R 219 Details of bonding type rmsd hydrogen bonds : bond 0.03035 ( 144) hydrogen bonds : angle 3.60304 ( 432) SS BOND : bond 0.00203 ( 2) SS BOND : angle 0.84188 ( 4) covalent geometry : bond 0.00217 ( 2302) covalent geometry : angle 0.48885 ( 3148) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.224 Fit side-chains REVERT: R 258 LYS cc_start: 0.8170 (ttpt) cc_final: 0.7853 (ttmt) outliers start: 4 outliers final: 2 residues processed: 28 average time/residue: 0.2362 time to fit residues: 7.4782 Evaluate side-chains 27 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 326 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 7 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.105515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.092903 restraints weight = 4048.713| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.02 r_work: 0.3136 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2304 Z= 0.108 Angle : 0.512 7.350 3152 Z= 0.257 Chirality : 0.038 0.117 366 Planarity : 0.003 0.021 385 Dihedral : 5.109 59.100 324 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.42 % Allowed : 25.59 % Favored : 72.99 % 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: 1.59 (0.54), residues: 290 helix: 2.04 (0.38), residues: 213 sheet: None (None), residues: 0 loop : -1.91 (0.73), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 317 HIS 0.001 0.000 HIS R 59 PHE 0.006 0.001 PHE R 206 TYR 0.014 0.001 TYR R 99 ARG 0.004 0.000 ARG R 219 Details of bonding type rmsd hydrogen bonds : bond 0.03388 ( 144) hydrogen bonds : angle 3.66001 ( 432) SS BOND : bond 0.00214 ( 2) SS BOND : angle 0.93073 ( 4) covalent geometry : bond 0.00241 ( 2302) covalent geometry : angle 0.51124 ( 3148) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.228 Fit side-chains REVERT: R 258 LYS cc_start: 0.8195 (ttpt) cc_final: 0.7891 (ttmt) outliers start: 3 outliers final: 3 residues processed: 28 average time/residue: 0.2332 time to fit residues: 7.4067 Evaluate side-chains 28 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 326 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.106133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.093408 restraints weight = 4023.731| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.01 r_work: 0.3145 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2304 Z= 0.103 Angle : 0.515 8.139 3152 Z= 0.258 Chirality : 0.038 0.116 366 Planarity : 0.003 0.021 385 Dihedral : 5.089 59.139 324 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.42 % Allowed : 26.07 % Favored : 72.51 % 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: 1.64 (0.54), residues: 290 helix: 2.09 (0.39), residues: 212 sheet: None (None), residues: 0 loop : -1.87 (0.73), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 317 HIS 0.001 0.000 HIS R 59 PHE 0.006 0.001 PHE R 206 TYR 0.014 0.001 TYR R 99 ARG 0.004 0.000 ARG R 219 Details of bonding type rmsd hydrogen bonds : bond 0.03120 ( 144) hydrogen bonds : angle 3.62201 ( 432) SS BOND : bond 0.00195 ( 2) SS BOND : angle 0.85959 ( 4) covalent geometry : bond 0.00225 ( 2302) covalent geometry : angle 0.51435 ( 3148) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1388.16 seconds wall clock time: 24 minutes 44.19 seconds (1484.19 seconds total)