Starting phenix.real_space_refine on Mon Nov 17 19:20:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uk5_26575/11_2025/7uk5_26575.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uk5_26575/11_2025/7uk5_26575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uk5_26575/11_2025/7uk5_26575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uk5_26575/11_2025/7uk5_26575.map" model { file = "/net/cci-nas-00/data/ceres_data/7uk5_26575/11_2025/7uk5_26575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uk5_26575/11_2025/7uk5_26575.cif" } resolution = 2.76 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= 0.005 sd= 0.072 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 K 4 8.98 5 S 56 5.16 5 C 5252 2.51 5 N 1332 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8000 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B, C, D Time building chain proxies: 1.68, per 1000 atoms: 0.21 Number of scatterers: 8000 At special positions: 0 Unit cell: (116.466, 116.466, 78.47, 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) K 4 19.00 S 56 16.00 O 1356 8.00 N 1332 7.00 C 5252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 431.4 milliseconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 83.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 166 through 177 Processing helix chain 'A' and resid 182 through 205 Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 225 through 250 Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 279 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 320 removed outlier: 3.518A pdb=" N ARG A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 347 Processing helix chain 'A' and resid 356 through 369 removed outlier: 4.095A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 399 Processing helix chain 'A' and resid 401 through 424 Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 182 through 205 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 225 through 250 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 260 through 279 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.518A pdb=" N ARG B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 4.095A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 399 Processing helix chain 'B' and resid 401 through 424 Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 182 through 205 Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 225 through 250 Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 260 through 279 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 307 through 320 removed outlier: 3.518A pdb=" N ARG C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 347 Processing helix chain 'C' and resid 356 through 369 removed outlier: 4.095A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 399 Processing helix chain 'C' and resid 401 through 424 Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 182 through 205 Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 225 through 250 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 279 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 320 removed outlier: 3.518A pdb=" N ARG D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 347 Processing helix chain 'D' and resid 356 through 369 removed outlier: 4.096A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 399 Processing helix chain 'D' and resid 401 through 424 633 hydrogen bonds defined for protein. 1815 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: 1.23 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2436 1.34 - 1.46: 2009 1.46 - 1.58: 3655 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 8188 Sorted by residual: bond pdb=" N ARG C 418 " pdb=" CA ARG C 418 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 4.01e+00 bond pdb=" N ARG A 418 " pdb=" CA ARG A 418 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 4.01e+00 bond pdb=" N ARG D 418 " pdb=" CA ARG D 418 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 4.01e+00 bond pdb=" N ARG B 418 " pdb=" CA ARG B 418 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.21e-02 6.83e+03 3.96e+00 bond pdb=" C GLN C 417 " pdb=" N ARG C 418 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.31e-02 5.83e+03 1.98e+00 ... (remaining 8183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 10372 1.00 - 1.99: 585 1.99 - 2.99: 115 2.99 - 3.98: 33 3.98 - 4.98: 19 Bond angle restraints: 11124 Sorted by residual: angle pdb=" CA TYR C 188 " pdb=" CB TYR C 188 " pdb=" CG TYR C 188 " ideal model delta sigma weight residual 113.90 118.18 -4.28 1.80e+00 3.09e-01 5.67e+00 angle pdb=" N THR B 182 " pdb=" CA THR B 182 " pdb=" C THR B 182 " ideal model delta sigma weight residual 113.41 110.51 2.90 1.22e+00 6.72e-01 5.66e+00 angle pdb=" CA TYR D 188 " pdb=" CB TYR D 188 " pdb=" CG TYR D 188 " ideal model delta sigma weight residual 113.90 118.18 -4.28 1.80e+00 3.09e-01 5.64e+00 angle pdb=" N THR A 182 " pdb=" CA THR A 182 " pdb=" C THR A 182 " ideal model delta sigma weight residual 113.41 110.53 2.88 1.22e+00 6.72e-01 5.58e+00 angle pdb=" CA TYR A 188 " pdb=" CB TYR A 188 " pdb=" CG TYR A 188 " ideal model delta sigma weight residual 113.90 118.15 -4.25 1.80e+00 3.09e-01 5.58e+00 ... (remaining 11119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4400 17.87 - 35.73: 336 35.73 - 53.60: 44 53.60 - 71.47: 4 71.47 - 89.34: 8 Dihedral angle restraints: 4792 sinusoidal: 1760 harmonic: 3032 Sorted by residual: dihedral pdb=" CG ARG D 411 " pdb=" CD ARG D 411 " pdb=" NE ARG D 411 " pdb=" CZ ARG D 411 " ideal model delta sinusoidal sigma weight residual 180.00 -136.89 -43.11 2 1.50e+01 4.44e-03 9.96e+00 dihedral pdb=" CG ARG C 411 " pdb=" CD ARG C 411 " pdb=" NE ARG C 411 " pdb=" CZ ARG C 411 " ideal model delta sinusoidal sigma weight residual 180.00 -136.91 -43.09 2 1.50e+01 4.44e-03 9.96e+00 dihedral pdb=" CG ARG B 411 " pdb=" CD ARG B 411 " pdb=" NE ARG B 411 " pdb=" CZ ARG B 411 " ideal model delta sinusoidal sigma weight residual 180.00 -136.91 -43.09 2 1.50e+01 4.44e-03 9.96e+00 ... (remaining 4789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 702 0.027 - 0.055: 352 0.055 - 0.082: 199 0.082 - 0.110: 41 0.110 - 0.137: 26 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CB VAL B 297 " pdb=" CA VAL B 297 " pdb=" CG1 VAL B 297 " pdb=" CG2 VAL B 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CB VAL C 297 " pdb=" CA VAL C 297 " pdb=" CG1 VAL C 297 " pdb=" CG2 VAL C 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CB VAL A 297 " pdb=" CA VAL A 297 " pdb=" CG1 VAL A 297 " pdb=" CG2 VAL A 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1317 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 417 " 0.017 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C GLN B 417 " -0.056 2.00e-02 2.50e+03 pdb=" O GLN B 417 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG B 418 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 417 " -0.017 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C GLN A 417 " 0.056 2.00e-02 2.50e+03 pdb=" O GLN A 417 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG A 418 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 417 " 0.017 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C GLN C 417 " -0.056 2.00e-02 2.50e+03 pdb=" O GLN C 417 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG C 418 " 0.019 2.00e-02 2.50e+03 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.74: 810 2.74 - 3.34: 10002 3.34 - 3.94: 15630 3.94 - 4.54: 21328 4.54 - 5.14: 32150 Nonbonded interactions: 79920 Sorted by model distance: nonbonded pdb=" OE2 GLU C 205 " pdb=" NH2 ARG C 296 " model vdw 2.139 3.120 nonbonded pdb=" OE2 GLU B 205 " pdb=" NH2 ARG B 296 " model vdw 2.139 3.120 nonbonded pdb=" OE2 GLU A 205 " pdb=" NH2 ARG A 296 " model vdw 2.139 3.120 nonbonded pdb=" OE2 GLU D 205 " pdb=" NH2 ARG D 296 " model vdw 2.139 3.120 nonbonded pdb=" O PHE D 257 " pdb=" OG SER D 260 " model vdw 2.343 3.040 ... (remaining 79915 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 166 through 424) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.830 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: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.880 Find NCS groups from input model: 0.140 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:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 0.029 8188 Z= 0.197 Angle : 0.581 4.978 11124 Z= 0.349 Chirality : 0.042 0.137 1320 Planarity : 0.006 0.049 1360 Dihedral : 12.964 89.336 2840 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.44 (0.27), residues: 1028 helix: 1.57 (0.18), residues: 800 sheet: None (None), residues: 0 loop : -1.21 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 418 TYR 0.020 0.002 TYR D 188 PHE 0.010 0.001 PHE B 289 TRP 0.004 0.001 TRP B 172 HIS 0.001 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 8188) covalent geometry : angle 0.58135 (11124) hydrogen bonds : bond 0.12175 ( 633) hydrogen bonds : angle 5.00289 ( 1815) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.300 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.5340 time to fit residues: 61.3688 Evaluate side-chains 96 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.165786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114664 restraints weight = 8637.525| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.92 r_work: 0.3232 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8188 Z= 0.183 Angle : 0.526 4.407 11124 Z= 0.296 Chirality : 0.042 0.133 1320 Planarity : 0.005 0.046 1360 Dihedral : 3.919 16.713 1148 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.90 % Allowed : 7.11 % Favored : 91.00 % 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: 2.03 (0.27), residues: 1028 helix: 1.83 (0.18), residues: 800 sheet: None (None), residues: 0 loop : -0.34 (0.45), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 256 TYR 0.018 0.002 TYR D 188 PHE 0.014 0.001 PHE A 257 TRP 0.007 0.002 TRP A 362 HIS 0.001 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 8188) covalent geometry : angle 0.52618 (11124) hydrogen bonds : bond 0.04703 ( 633) hydrogen bonds : angle 3.99768 ( 1815) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.332 Fit side-chains outliers start: 16 outliers final: 16 residues processed: 104 average time/residue: 0.5239 time to fit residues: 58.0697 Evaluate side-chains 113 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain D residue 347 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 51 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 78 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.168745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.117959 restraints weight = 8592.675| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.92 r_work: 0.3275 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8188 Z= 0.122 Angle : 0.472 4.518 11124 Z= 0.261 Chirality : 0.039 0.120 1320 Planarity : 0.005 0.049 1360 Dihedral : 3.620 14.458 1148 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.95 % Allowed : 9.72 % Favored : 89.34 % 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: 2.53 (0.28), residues: 1028 helix: 2.17 (0.19), residues: 800 sheet: None (None), residues: 0 loop : -0.04 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 418 TYR 0.018 0.001 TYR B 188 PHE 0.011 0.001 PHE A 257 TRP 0.005 0.001 TRP A 362 HIS 0.001 0.000 HIS D 306 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8188) covalent geometry : angle 0.47205 (11124) hydrogen bonds : bond 0.04092 ( 633) hydrogen bonds : angle 3.83315 ( 1815) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.332 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 116 average time/residue: 0.5054 time to fit residues: 62.6393 Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.164634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113393 restraints weight = 8723.569| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.94 r_work: 0.3220 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8188 Z= 0.214 Angle : 0.539 4.513 11124 Z= 0.297 Chirality : 0.043 0.134 1320 Planarity : 0.005 0.048 1360 Dihedral : 3.878 16.142 1148 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.90 % Allowed : 9.95 % Favored : 88.15 % 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 (0.27), residues: 1028 helix: 1.96 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.26 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 418 TYR 0.018 0.002 TYR B 188 PHE 0.012 0.002 PHE D 257 TRP 0.007 0.002 TRP D 172 HIS 0.001 0.000 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 8188) covalent geometry : angle 0.53900 (11124) hydrogen bonds : bond 0.04761 ( 633) hydrogen bonds : angle 3.91314 ( 1815) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.280 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 104 average time/residue: 0.5376 time to fit residues: 59.5398 Evaluate side-chains 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.166665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.116466 restraints weight = 8684.867| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.88 r_work: 0.3249 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8188 Z= 0.148 Angle : 0.487 4.532 11124 Z= 0.271 Chirality : 0.040 0.124 1320 Planarity : 0.005 0.049 1360 Dihedral : 3.710 15.116 1148 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.42 % Allowed : 10.90 % Favored : 87.68 % 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: 2.45 (0.28), residues: 1028 helix: 2.12 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.15 (0.48), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 418 TYR 0.017 0.002 TYR B 188 PHE 0.010 0.001 PHE A 257 TRP 0.005 0.001 TRP C 172 HIS 0.001 0.000 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8188) covalent geometry : angle 0.48688 (11124) hydrogen bonds : bond 0.04249 ( 633) hydrogen bonds : angle 3.84069 ( 1815) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.304 Fit side-chains REVERT: A 396 LEU cc_start: 0.5953 (mp) cc_final: 0.5338 (tm) REVERT: B 396 LEU cc_start: 0.5928 (mp) cc_final: 0.5313 (tm) REVERT: C 396 LEU cc_start: 0.5929 (mp) cc_final: 0.5314 (tm) REVERT: D 396 LEU cc_start: 0.5939 (mp) cc_final: 0.5321 (tm) outliers start: 12 outliers final: 12 residues processed: 97 average time/residue: 0.5741 time to fit residues: 59.1764 Evaluate side-chains 105 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 30 optimal weight: 0.0670 chunk 51 optimal weight: 0.0020 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.0170 chunk 28 optimal weight: 0.9980 overall best weight: 0.2964 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.171759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121693 restraints weight = 8664.208| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.91 r_work: 0.3315 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8188 Z= 0.106 Angle : 0.448 4.434 11124 Z= 0.246 Chirality : 0.038 0.112 1320 Planarity : 0.005 0.051 1360 Dihedral : 3.407 12.627 1148 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.90 % Allowed : 11.73 % Favored : 86.37 % 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: 2.73 (0.28), residues: 1028 helix: 2.36 (0.19), residues: 800 sheet: None (None), residues: 0 loop : -0.20 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 299 TYR 0.015 0.001 TYR B 188 PHE 0.008 0.001 PHE A 257 TRP 0.003 0.001 TRP A 172 HIS 0.001 0.000 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8188) covalent geometry : angle 0.44781 (11124) hydrogen bonds : bond 0.03721 ( 633) hydrogen bonds : angle 3.74526 ( 1815) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.276 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 112 average time/residue: 0.5521 time to fit residues: 65.8036 Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 54 optimal weight: 0.0070 chunk 4 optimal weight: 0.0040 chunk 12 optimal weight: 0.9990 chunk 71 optimal weight: 0.0020 chunk 68 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 overall best weight: 0.3218 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.170749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.120966 restraints weight = 8745.774| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.91 r_work: 0.3313 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8188 Z= 0.109 Angle : 0.449 4.655 11124 Z= 0.246 Chirality : 0.038 0.114 1320 Planarity : 0.005 0.052 1360 Dihedral : 3.325 12.057 1148 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.42 % Allowed : 11.49 % Favored : 87.09 % 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: 2.83 (0.28), residues: 1028 helix: 2.43 (0.19), residues: 800 sheet: None (None), residues: 0 loop : -0.17 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 299 TYR 0.014 0.001 TYR B 188 PHE 0.008 0.001 PHE C 257 TRP 0.004 0.001 TRP D 362 HIS 0.001 0.000 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8188) covalent geometry : angle 0.44873 (11124) hydrogen bonds : bond 0.03744 ( 633) hydrogen bonds : angle 3.70886 ( 1815) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.308 Fit side-chains REVERT: A 279 MET cc_start: 0.5149 (mtm) cc_final: 0.4606 (ptm) REVERT: B 279 MET cc_start: 0.5104 (mtm) cc_final: 0.4524 (ptm) REVERT: C 279 MET cc_start: 0.5095 (mtm) cc_final: 0.4514 (ptm) REVERT: D 279 MET cc_start: 0.5085 (mtm) cc_final: 0.4507 (ptm) outliers start: 12 outliers final: 8 residues processed: 109 average time/residue: 0.5121 time to fit residues: 59.6029 Evaluate side-chains 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 0.0570 chunk 46 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.168550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119008 restraints weight = 8748.284| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.88 r_work: 0.3262 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8188 Z= 0.133 Angle : 0.477 4.714 11124 Z= 0.261 Chirality : 0.039 0.119 1320 Planarity : 0.005 0.052 1360 Dihedral : 3.418 12.975 1148 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.78 % Allowed : 11.61 % Favored : 86.61 % 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: 2.75 (0.28), residues: 1028 helix: 2.34 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.06 (0.48), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 418 TYR 0.014 0.001 TYR A 188 PHE 0.009 0.001 PHE C 257 TRP 0.006 0.001 TRP A 362 HIS 0.001 0.000 HIS D 179 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8188) covalent geometry : angle 0.47717 (11124) hydrogen bonds : bond 0.03975 ( 633) hydrogen bonds : angle 3.75857 ( 1815) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.333 Fit side-chains REVERT: A 279 MET cc_start: 0.5146 (mtm) cc_final: 0.4644 (ptm) REVERT: B 279 MET cc_start: 0.5081 (mtm) cc_final: 0.4551 (ptm) REVERT: C 279 MET cc_start: 0.5090 (mtm) cc_final: 0.4557 (ptm) REVERT: D 279 MET cc_start: 0.5080 (mtm) cc_final: 0.4552 (ptm) outliers start: 15 outliers final: 8 residues processed: 100 average time/residue: 0.5494 time to fit residues: 58.5405 Evaluate side-chains 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 0.1980 chunk 75 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.169703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119535 restraints weight = 8592.680| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.92 r_work: 0.3288 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8188 Z= 0.128 Angle : 0.478 4.889 11124 Z= 0.261 Chirality : 0.039 0.118 1320 Planarity : 0.005 0.052 1360 Dihedral : 3.399 12.738 1148 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.95 % Allowed : 12.56 % Favored : 86.49 % 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: 2.73 (0.28), residues: 1028 helix: 2.32 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.08 (0.48), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 299 TYR 0.012 0.001 TYR B 188 PHE 0.009 0.001 PHE C 257 TRP 0.004 0.001 TRP A 362 HIS 0.001 0.000 HIS D 179 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8188) covalent geometry : angle 0.47771 (11124) hydrogen bonds : bond 0.03933 ( 633) hydrogen bonds : angle 3.76572 ( 1815) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.300 Fit side-chains REVERT: A 279 MET cc_start: 0.5127 (mtm) cc_final: 0.4702 (ptm) REVERT: B 279 MET cc_start: 0.5113 (mtm) cc_final: 0.4648 (ptm) REVERT: C 279 MET cc_start: 0.5130 (mtm) cc_final: 0.4659 (ptm) REVERT: D 279 MET cc_start: 0.5112 (mtm) cc_final: 0.4654 (ptm) outliers start: 8 outliers final: 8 residues processed: 100 average time/residue: 0.5445 time to fit residues: 57.9664 Evaluate side-chains 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 29 optimal weight: 0.0570 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.168433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.118835 restraints weight = 8708.358| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.87 r_work: 0.3280 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8188 Z= 0.134 Angle : 0.488 5.191 11124 Z= 0.267 Chirality : 0.039 0.122 1320 Planarity : 0.005 0.051 1360 Dihedral : 3.436 13.026 1148 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.95 % Allowed : 12.44 % Favored : 86.61 % 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: 2.71 (0.28), residues: 1028 helix: 2.33 (0.19), residues: 800 sheet: None (None), residues: 0 loop : -0.13 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 254 TYR 0.012 0.001 TYR A 188 PHE 0.009 0.001 PHE C 257 TRP 0.005 0.001 TRP A 362 HIS 0.001 0.000 HIS C 179 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8188) covalent geometry : angle 0.48786 (11124) hydrogen bonds : bond 0.04018 ( 633) hydrogen bonds : angle 3.79053 ( 1815) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.358 Fit side-chains REVERT: A 279 MET cc_start: 0.5165 (mtm) cc_final: 0.4771 (ptm) REVERT: B 279 MET cc_start: 0.5246 (mtm) cc_final: 0.4767 (ptm) REVERT: C 279 MET cc_start: 0.5265 (mtm) cc_final: 0.4781 (ptm) REVERT: D 279 MET cc_start: 0.5251 (mtm) cc_final: 0.4773 (ptm) outliers start: 8 outliers final: 8 residues processed: 100 average time/residue: 0.5498 time to fit residues: 58.5845 Evaluate side-chains 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 333 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 21 optimal weight: 0.0570 chunk 72 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.169325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120347 restraints weight = 8682.431| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.84 r_work: 0.3277 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8188 Z= 0.122 Angle : 0.477 4.995 11124 Z= 0.261 Chirality : 0.039 0.120 1320 Planarity : 0.005 0.052 1360 Dihedral : 3.383 12.650 1148 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.95 % Allowed : 12.44 % Favored : 86.61 % 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: 2.75 (0.28), residues: 1028 helix: 2.32 (0.19), residues: 804 sheet: None (None), residues: 0 loop : 0.02 (0.48), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 418 TYR 0.012 0.001 TYR B 188 PHE 0.009 0.001 PHE C 257 TRP 0.004 0.001 TRP D 172 HIS 0.001 0.000 HIS D 179 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8188) covalent geometry : angle 0.47662 (11124) hydrogen bonds : bond 0.03906 ( 633) hydrogen bonds : angle 3.78706 ( 1815) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3099.57 seconds wall clock time: 53 minutes 33.78 seconds (3213.78 seconds total)