Starting phenix.real_space_refine on Tue Mar 3 11:44:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lcj_23275/03_2026/7lcj_23275.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lcj_23275/03_2026/7lcj_23275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lcj_23275/03_2026/7lcj_23275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lcj_23275/03_2026/7lcj_23275.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lcj_23275/03_2026/7lcj_23275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lcj_23275/03_2026/7lcj_23275.map" } resolution = 2.82 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= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 18 5.16 5 C 2148 2.51 5 N 526 2.21 5 O 571 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3264 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3206 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 375} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 58 Unusual residues: {'UK4': 1} Classifications: {'undetermined': 1, 'water': 17} Link IDs: {None: 17} Time building chain proxies: 1.04, per 1000 atoms: 0.32 Number of scatterers: 3264 At special positions: 0 Unit cell: (60.079, 116.866, 69.955, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 F 1 9.00 O 571 8.00 N 526 7.00 C 2148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.02 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 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: 0.28 Conformation dependent library (CDL) restraints added in 123.2 milliseconds 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 2 sheets defined 70.0% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'R' and resid 31 through 53 removed outlier: 3.918A pdb=" N GLU R 41 " --> pdb=" O GLN R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 169 removed outlier: 3.604A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 201 Processing helix chain 'R' and resid 202 through 207 removed outlier: 3.510A pdb=" N SER R 206 " --> pdb=" O LYS R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 222 removed outlier: 3.944A pdb=" N ASP R 215 " --> pdb=" O GLN R 211 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY R 216 " --> pdb=" O HIS R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 257 Processing helix chain 'R' and resid 263 through 276 removed outlier: 3.705A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 291 removed outlier: 3.800A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 306 through 338 Proline residue: R 312 - end of helix removed outlier: 3.848A pdb=" N ASN R 338 " --> pdb=" O LYS R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 363 through 371 Processing helix chain 'R' and resid 377 through 392 Processing helix chain 'R' and resid 393 through 404 Processing helix chain 'R' and resid 406 through 423 removed outlier: 3.547A pdb=" N TRP R 420 " --> pdb=" O SER R 416 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU R 423 " --> pdb=" O ARG R 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 79 through 80 removed outlier: 3.812A pdb=" N SER R 79 " --> pdb=" O CYS R 104 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS R 104 " --> pdb=" O SER R 79 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL R 100 " --> pdb=" O VAL R 83 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL R 83 " --> pdb=" O VAL R 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'R' and resid 79 through 80 removed outlier: 3.812A pdb=" N SER R 79 " --> pdb=" O CYS R 104 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N CYS R 104 " --> pdb=" O SER R 79 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 597 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: 0.47 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 487 1.27 - 1.41: 974 1.41 - 1.54: 1861 1.54 - 1.68: 6 1.68 - 1.82: 23 Bond restraints: 3351 Sorted by residual: bond pdb=" C27 UK4 R 501 " pdb=" C28 UK4 R 501 " ideal model delta sigma weight residual 1.535 1.421 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C38 UK4 R 501 " pdb=" C39 UK4 R 501 " ideal model delta sigma weight residual 1.427 1.525 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C28 UK4 R 501 " pdb=" C29 UK4 R 501 " ideal model delta sigma weight residual 1.529 1.447 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C LEU R 89 " pdb=" N PRO R 90 " ideal model delta sigma weight residual 1.335 1.380 -0.045 1.28e-02 6.10e+03 1.24e+01 bond pdb=" C TRP R 72 " pdb=" N PRO R 73 " ideal model delta sigma weight residual 1.326 1.375 -0.049 1.44e-02 4.82e+03 1.17e+01 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 4503 3.63 - 7.26: 63 7.26 - 10.88: 3 10.88 - 14.51: 1 14.51 - 18.14: 1 Bond angle restraints: 4571 Sorted by residual: angle pdb=" C SER R 136 " pdb=" N PRO R 137 " pdb=" CA PRO R 137 " ideal model delta sigma weight residual 119.28 126.40 -7.12 1.10e+00 8.26e-01 4.19e+01 angle pdb=" C THR R 362 " pdb=" CA THR R 362 " pdb=" CB THR R 362 " ideal model delta sigma weight residual 110.67 122.36 -11.69 1.92e+00 2.71e-01 3.71e+01 angle pdb=" C08 UK4 R 501 " pdb=" C09 UK4 R 501 " pdb=" C32 UK4 R 501 " ideal model delta sigma weight residual 110.26 92.12 18.14 3.00e+00 1.11e-01 3.66e+01 angle pdb=" C LEU R 89 " pdb=" N PRO R 90 " pdb=" CA PRO R 90 " ideal model delta sigma weight residual 119.28 125.52 -6.24 1.10e+00 8.26e-01 3.21e+01 angle pdb=" C TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta sigma weight residual 110.79 119.63 -8.84 1.66e+00 3.63e-01 2.83e+01 ... (remaining 4566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 1743 17.85 - 35.70: 157 35.70 - 53.55: 27 53.55 - 71.39: 3 71.39 - 89.24: 2 Dihedral angle restraints: 1932 sinusoidal: 776 harmonic: 1156 Sorted by residual: dihedral pdb=" C THR R 362 " pdb=" N THR R 362 " pdb=" CA THR R 362 " pdb=" CB THR R 362 " ideal model delta harmonic sigma weight residual -122.00 -143.04 21.04 0 2.50e+00 1.60e-01 7.08e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -142.72 56.72 1 1.00e+01 1.00e-02 4.33e+01 dihedral pdb=" C TYR R 148 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta harmonic sigma weight residual -122.60 -138.17 15.57 0 2.50e+00 1.60e-01 3.88e+01 ... (remaining 1929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 466 0.145 - 0.290: 27 0.290 - 0.435: 2 0.435 - 0.580: 1 0.580 - 0.724: 1 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA THR R 362 " pdb=" N THR R 362 " pdb=" C THR R 362 " pdb=" CB THR R 362 " both_signs ideal model delta sigma weight residual False 2.53 1.80 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA TYR R 148 " pdb=" N TYR R 148 " pdb=" C TYR R 148 " pdb=" CB TYR R 148 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.02e+00 chirality pdb=" CA TRP R 243 " pdb=" N TRP R 243 " pdb=" C TRP R 243 " pdb=" CB TRP R 243 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 494 not shown) Planarity restraints: 557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 355 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C THR R 355 " -0.045 2.00e-02 2.50e+03 pdb=" O THR R 355 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU R 356 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 146 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.47e+00 pdb=" C ILE R 146 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE R 146 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE R 147 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 276 " 0.033 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO R 277 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO R 277 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 277 " 0.027 5.00e-02 4.00e+02 ... (remaining 554 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 437 2.75 - 3.29: 3196 3.29 - 3.83: 5221 3.83 - 4.36: 6319 4.36 - 4.90: 10614 Nonbonded interactions: 25787 Sorted by model distance: nonbonded pdb=" O LYS R 342 " pdb=" NZ LYS R 346 " model vdw 2.216 3.120 nonbonded pdb=" O GLY R 98 " pdb=" ND1 HIS R 99 " model vdw 2.335 3.120 nonbonded pdb=" O GLU R 408 " pdb=" OE1 GLU R 412 " model vdw 2.335 3.040 nonbonded pdb=" OE2 GLU R 76 " pdb=" OG SER R 79 " model vdw 2.342 3.040 nonbonded pdb=" OD1 ASN R 300 " pdb=" N SER R 301 " model vdw 2.383 3.120 ... (remaining 25782 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: 1.360 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.790 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:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 : 0.011 0.114 3355 Z= 0.600 Angle : 1.187 18.141 4579 Z= 0.785 Chirality : 0.083 0.724 497 Planarity : 0.006 0.049 557 Dihedral : 13.407 89.243 1172 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.16 % Allowed : 1.16 % Favored : 97.67 % Cbeta Deviations : 0.80 % 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 are not related in a simple way. whole: 0.54 (0.41), residues: 386 helix: 1.08 (0.32), residues: 247 sheet: None (None), residues: 0 loop : -0.90 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 299 TYR 0.023 0.003 TYR R 148 PHE 0.017 0.003 PHE R 280 TRP 0.019 0.002 TRP R 243 HIS 0.006 0.002 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.01051 ( 3351) covalent geometry : angle 1.18750 ( 4571) SS BOND : bond 0.00473 ( 4) SS BOND : angle 1.07309 ( 8) hydrogen bonds : bond 0.19748 ( 199) hydrogen bonds : angle 6.40481 ( 597) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.114 Fit side-chains REVERT: R 41 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6643 (mm-30) REVERT: R 416 SER cc_start: 0.6812 (t) cc_final: 0.6581 (m) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.4881 time to fit residues: 18.2500 Evaluate side-chains 29 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 204 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.0010 chunk 37 optimal weight: 0.6980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 GLN ** R 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.204938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.134811 restraints weight = 3306.818| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.12 r_work: 0.3371 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3355 Z= 0.138 Angle : 0.572 7.227 4579 Z= 0.306 Chirality : 0.037 0.127 497 Planarity : 0.004 0.050 557 Dihedral : 5.219 28.819 458 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.45 % Allowed : 7.85 % Favored : 90.70 % 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 are not related in a simple way. whole: 1.66 (0.42), residues: 386 helix: 2.03 (0.32), residues: 256 sheet: None (None), residues: 0 loop : -0.81 (0.50), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 414 TYR 0.028 0.002 TYR R 148 PHE 0.015 0.001 PHE R 143 TRP 0.016 0.001 TRP R 243 HIS 0.005 0.001 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 3351) covalent geometry : angle 0.57158 ( 4571) SS BOND : bond 0.00157 ( 4) SS BOND : angle 0.82808 ( 8) hydrogen bonds : bond 0.06847 ( 199) hydrogen bonds : angle 3.94443 ( 597) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.118 Fit side-chains REVERT: R 41 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6982 (mp0) outliers start: 5 outliers final: 3 residues processed: 30 average time/residue: 0.4053 time to fit residues: 12.7289 Evaluate side-chains 25 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.203400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.133171 restraints weight = 3291.770| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.10 r_work: 0.3331 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3355 Z= 0.136 Angle : 0.536 7.294 4579 Z= 0.281 Chirality : 0.037 0.133 497 Planarity : 0.004 0.057 557 Dihedral : 4.852 30.644 456 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.45 % Allowed : 10.76 % Favored : 87.79 % 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 are not related in a simple way. whole: 1.95 (0.43), residues: 386 helix: 2.26 (0.32), residues: 256 sheet: None (None), residues: 0 loop : -0.70 (0.51), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 102 TYR 0.028 0.002 TYR R 148 PHE 0.011 0.001 PHE R 280 TRP 0.020 0.001 TRP R 243 HIS 0.005 0.001 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 3351) covalent geometry : angle 0.53563 ( 4571) SS BOND : bond 0.00183 ( 4) SS BOND : angle 0.68814 ( 8) hydrogen bonds : bond 0.06772 ( 199) hydrogen bonds : angle 3.81302 ( 597) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.090 Fit side-chains REVERT: R 41 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6836 (mm-30) outliers start: 5 outliers final: 4 residues processed: 27 average time/residue: 0.3738 time to fit residues: 10.5801 Evaluate side-chains 28 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 370 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 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 = 0.4222 r_free = 0.4222 target = 0.203383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133173 restraints weight = 3284.064| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.09 r_work: 0.3326 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3355 Z= 0.129 Angle : 0.522 9.898 4579 Z= 0.271 Chirality : 0.037 0.127 497 Planarity : 0.004 0.059 557 Dihedral : 4.711 30.361 456 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.03 % Allowed : 12.21 % Favored : 85.76 % 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 are not related in a simple way. whole: 2.15 (0.43), residues: 386 helix: 2.41 (0.32), residues: 256 sheet: None (None), residues: 0 loop : -0.64 (0.52), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 414 TYR 0.026 0.001 TYR R 148 PHE 0.010 0.001 PHE R 280 TRP 0.019 0.001 TRP R 243 HIS 0.004 0.001 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3351) covalent geometry : angle 0.52190 ( 4571) SS BOND : bond 0.00181 ( 4) SS BOND : angle 0.60581 ( 8) hydrogen bonds : bond 0.06258 ( 199) hydrogen bonds : angle 3.70727 ( 597) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.132 Fit side-chains REVERT: R 41 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6836 (mm-30) REVERT: R 201 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7201 (pt) REVERT: R 384 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7864 (mm) outliers start: 7 outliers final: 4 residues processed: 30 average time/residue: 0.4197 time to fit residues: 13.1702 Evaluate side-chains 30 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 7 optimal weight: 20.0000 chunk 12 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.200622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.129861 restraints weight = 3301.171| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.11 r_work: 0.3315 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3355 Z= 0.159 Angle : 0.555 10.189 4579 Z= 0.287 Chirality : 0.038 0.132 497 Planarity : 0.004 0.060 557 Dihedral : 4.809 30.420 456 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.33 % Allowed : 11.92 % Favored : 85.76 % 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 are not related in a simple way. whole: 1.98 (0.43), residues: 386 helix: 2.23 (0.32), residues: 258 sheet: None (None), residues: 0 loop : -0.64 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 414 TYR 0.027 0.002 TYR R 148 PHE 0.012 0.001 PHE R 280 TRP 0.020 0.001 TRP R 243 HIS 0.002 0.001 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 3351) covalent geometry : angle 0.55516 ( 4571) SS BOND : bond 0.00230 ( 4) SS BOND : angle 0.54722 ( 8) hydrogen bonds : bond 0.07201 ( 199) hydrogen bonds : angle 3.80616 ( 597) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.103 Fit side-chains REVERT: R 41 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6921 (mm-30) REVERT: R 201 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7350 (pt) outliers start: 8 outliers final: 7 residues processed: 33 average time/residue: 0.3682 time to fit residues: 12.7301 Evaluate side-chains 33 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.204814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.133032 restraints weight = 3268.057| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.15 r_work: 0.3349 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3355 Z= 0.126 Angle : 0.510 9.623 4579 Z= 0.264 Chirality : 0.036 0.125 497 Planarity : 0.004 0.059 557 Dihedral : 4.666 30.842 456 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.62 % Allowed : 13.95 % Favored : 83.43 % 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 are not related in a simple way. whole: 2.22 (0.43), residues: 386 helix: 2.45 (0.32), residues: 258 sheet: None (None), residues: 0 loop : -0.60 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 414 TYR 0.024 0.001 TYR R 148 PHE 0.010 0.001 PHE R 280 TRP 0.019 0.001 TRP R 243 HIS 0.002 0.000 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 3351) covalent geometry : angle 0.50997 ( 4571) SS BOND : bond 0.00149 ( 4) SS BOND : angle 0.58762 ( 8) hydrogen bonds : bond 0.06198 ( 199) hydrogen bonds : angle 3.68015 ( 597) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.118 Fit side-chains REVERT: R 41 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7001 (mm-30) REVERT: R 159 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7754 (mt) REVERT: R 201 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7219 (pt) REVERT: R 384 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7908 (mm) outliers start: 9 outliers final: 5 residues processed: 33 average time/residue: 0.3674 time to fit residues: 12.7458 Evaluate side-chains 33 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.202531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131884 restraints weight = 3298.715| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.11 r_work: 0.3336 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3355 Z= 0.130 Angle : 0.514 9.660 4579 Z= 0.265 Chirality : 0.036 0.126 497 Planarity : 0.004 0.059 557 Dihedral : 4.644 30.999 456 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.20 % Allowed : 14.24 % Favored : 82.56 % 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 are not related in a simple way. whole: 2.28 (0.42), residues: 386 helix: 2.47 (0.32), residues: 258 sheet: None (None), residues: 0 loop : -0.54 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 414 TYR 0.025 0.001 TYR R 148 PHE 0.010 0.001 PHE R 280 TRP 0.018 0.001 TRP R 243 HIS 0.002 0.001 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3351) covalent geometry : angle 0.51355 ( 4571) SS BOND : bond 0.00166 ( 4) SS BOND : angle 0.52939 ( 8) hydrogen bonds : bond 0.06272 ( 199) hydrogen bonds : angle 3.67480 ( 597) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.126 Fit side-chains REVERT: R 41 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6978 (mm-30) REVERT: R 159 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7718 (mt) REVERT: R 201 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7242 (pt) REVERT: R 384 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7903 (mm) outliers start: 11 outliers final: 7 residues processed: 35 average time/residue: 0.3312 time to fit residues: 12.2372 Evaluate side-chains 36 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Chi-restraints excluded: chain R residue 416 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 0.5980 chunk 9 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 30.0000 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.202736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.129773 restraints weight = 3367.623| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.24 r_work: 0.3272 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3355 Z= 0.147 Angle : 0.533 10.051 4579 Z= 0.276 Chirality : 0.037 0.129 497 Planarity : 0.004 0.058 557 Dihedral : 4.724 30.755 456 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.91 % Allowed : 14.83 % Favored : 82.27 % 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 are not related in a simple way. whole: 2.23 (0.42), residues: 386 helix: 2.42 (0.32), residues: 258 sheet: None (None), residues: 0 loop : -0.53 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 414 TYR 0.026 0.002 TYR R 148 PHE 0.012 0.001 PHE R 280 TRP 0.018 0.001 TRP R 243 HIS 0.002 0.001 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3351) covalent geometry : angle 0.53310 ( 4571) SS BOND : bond 0.00179 ( 4) SS BOND : angle 0.49284 ( 8) hydrogen bonds : bond 0.06878 ( 199) hydrogen bonds : angle 3.75242 ( 597) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.130 Fit side-chains REVERT: R 41 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6952 (mm-30) REVERT: R 159 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7790 (mt) REVERT: R 201 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7336 (pt) REVERT: R 384 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7915 (mm) outliers start: 10 outliers final: 7 residues processed: 33 average time/residue: 0.3250 time to fit residues: 11.3065 Evaluate side-chains 36 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Chi-restraints excluded: chain R residue 416 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.204816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.132057 restraints weight = 3303.000| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.23 r_work: 0.3341 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3355 Z= 0.119 Angle : 0.499 9.501 4579 Z= 0.258 Chirality : 0.036 0.124 497 Planarity : 0.004 0.059 557 Dihedral : 4.583 30.189 456 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.62 % Allowed : 15.41 % Favored : 81.98 % 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 are not related in a simple way. whole: 2.43 (0.43), residues: 386 helix: 2.59 (0.32), residues: 258 sheet: None (None), residues: 0 loop : -0.48 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 414 TYR 0.024 0.001 TYR R 148 PHE 0.010 0.001 PHE R 280 TRP 0.018 0.001 TRP R 243 HIS 0.001 0.000 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 3351) covalent geometry : angle 0.49851 ( 4571) SS BOND : bond 0.00146 ( 4) SS BOND : angle 0.56094 ( 8) hydrogen bonds : bond 0.05920 ( 199) hydrogen bonds : angle 3.63781 ( 597) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.112 Fit side-chains REVERT: R 41 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6943 (mm-30) REVERT: R 159 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7652 (mt) REVERT: R 384 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7838 (mm) REVERT: R 414 ARG cc_start: 0.6213 (mmt90) cc_final: 0.5944 (mtt90) outliers start: 9 outliers final: 6 residues processed: 32 average time/residue: 0.3126 time to fit residues: 10.5925 Evaluate side-chains 34 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Chi-restraints excluded: chain R residue 416 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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 = 0.4197 r_free = 0.4197 target = 0.200604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.129984 restraints weight = 3277.255| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.11 r_work: 0.3321 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3355 Z= 0.152 Angle : 0.530 8.184 4579 Z= 0.276 Chirality : 0.038 0.130 497 Planarity : 0.004 0.058 557 Dihedral : 4.733 30.537 456 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.62 % Allowed : 15.41 % Favored : 81.98 % 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 are not related in a simple way. whole: 2.27 (0.42), residues: 386 helix: 2.43 (0.32), residues: 258 sheet: None (None), residues: 0 loop : -0.47 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 414 TYR 0.026 0.002 TYR R 148 PHE 0.012 0.001 PHE R 280 TRP 0.018 0.001 TRP R 243 HIS 0.002 0.001 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 3351) covalent geometry : angle 0.52974 ( 4571) SS BOND : bond 0.00197 ( 4) SS BOND : angle 0.47704 ( 8) hydrogen bonds : bond 0.06959 ( 199) hydrogen bonds : angle 3.74596 ( 597) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.128 Fit side-chains REVERT: R 41 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6911 (mm-30) REVERT: R 159 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7744 (mt) REVERT: R 384 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7924 (mm) outliers start: 9 outliers final: 7 residues processed: 32 average time/residue: 0.3224 time to fit residues: 10.9286 Evaluate side-chains 35 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 333 SER Chi-restraints excluded: chain R residue 370 VAL Chi-restraints excluded: chain R residue 384 LEU Chi-restraints excluded: chain R residue 416 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.201663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.131180 restraints weight = 3300.670| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.11 r_work: 0.3326 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3355 Z= 0.140 Angle : 0.516 8.256 4579 Z= 0.269 Chirality : 0.037 0.128 497 Planarity : 0.004 0.058 557 Dihedral : 4.687 30.334 456 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.62 % Allowed : 15.41 % Favored : 81.98 % 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 are not related in a simple way. whole: 2.33 (0.43), residues: 386 helix: 2.49 (0.32), residues: 258 sheet: None (None), residues: 0 loop : -0.47 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 414 TYR 0.025 0.002 TYR R 148 PHE 0.012 0.001 PHE R 280 TRP 0.018 0.001 TRP R 243 HIS 0.002 0.001 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 3351) covalent geometry : angle 0.51593 ( 4571) SS BOND : bond 0.00169 ( 4) SS BOND : angle 0.52028 ( 8) hydrogen bonds : bond 0.06594 ( 199) hydrogen bonds : angle 3.70101 ( 597) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1445.70 seconds wall clock time: 25 minutes 16.04 seconds (1516.04 seconds total)