Starting phenix.real_space_refine on Tue Mar 3 12:01:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zj2_14739/03_2026/7zj2_14739.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zj2_14739/03_2026/7zj2_14739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zj2_14739/03_2026/7zj2_14739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zj2_14739/03_2026/7zj2_14739.map" model { file = "/net/cci-nas-00/data/ceres_data/7zj2_14739/03_2026/7zj2_14739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zj2_14739/03_2026/7zj2_14739.cif" } resolution = 3.32 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= 0.032 sd= 0.409 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 2292 2.51 5 N 696 2.21 5 O 792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 3792 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 316 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 0.31, per 1000 atoms: 0.08 Number of scatterers: 3792 At special positions: 0 Unit cell: (73.84, 75.92, 47.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 792 8.00 N 696 7.00 C 2292 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: 0.26 Conformation dependent library (CDL) restraints added in 177.3 milliseconds 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 696 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 2 sheets defined 0.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 272 removed outlier: 6.560A pdb=" N GLN A 269 " --> pdb=" O SER C 270 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N ASN C 272 " --> pdb=" O GLN A 269 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER A 271 " --> pdb=" O ASN C 272 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN C 269 " --> pdb=" O SER E 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN E 272 " --> pdb=" O GLN C 269 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER C 271 " --> pdb=" O ASN E 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN E 269 " --> pdb=" O SER G 270 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N ASN G 272 " --> pdb=" O GLN E 269 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER E 271 " --> pdb=" O ASN G 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN G 269 " --> pdb=" O SER I 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN I 272 " --> pdb=" O GLN G 269 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER G 271 " --> pdb=" O ASN I 272 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN I 269 " --> pdb=" O SER K 270 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N ASN K 272 " --> pdb=" O GLN I 269 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER I 271 " --> pdb=" O ASN K 272 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 272 removed outlier: 6.560A pdb=" N GLN B 269 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN D 272 " --> pdb=" O GLN B 269 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER B 271 " --> pdb=" O ASN D 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN D 269 " --> pdb=" O SER F 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN F 272 " --> pdb=" O GLN D 269 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER D 271 " --> pdb=" O ASN F 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN F 269 " --> pdb=" O SER H 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN H 272 " --> pdb=" O GLN F 269 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER F 271 " --> pdb=" O ASN H 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN H 269 " --> pdb=" O SER J 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN J 272 " --> pdb=" O GLN H 269 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER H 271 " --> pdb=" O ASN J 272 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN J 269 " --> pdb=" O SER L 270 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ASN L 272 " --> pdb=" O GLN J 269 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER J 271 " --> pdb=" O ASN L 272 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 No hydrogen bonds 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: 0.02 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: 1.18 - 1.31: 672 1.31 - 1.43: 1368 1.43 - 1.56: 1836 1.56 - 1.68: 0 1.68 - 1.81: 24 Bond restraints: 3900 Sorted by residual: bond pdb=" C PRO L 288 " pdb=" O PRO L 288 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.16e-02 7.43e+03 1.99e+01 bond pdb=" C PRO I 288 " pdb=" O PRO I 288 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.16e-02 7.43e+03 1.99e+01 bond pdb=" C PRO A 288 " pdb=" O PRO A 288 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.16e-02 7.43e+03 1.99e+01 bond pdb=" C PRO E 288 " pdb=" O PRO E 288 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.16e-02 7.43e+03 1.98e+01 bond pdb=" C PRO F 288 " pdb=" O PRO F 288 " ideal model delta sigma weight residual 1.233 1.181 0.052 1.16e-02 7.43e+03 1.98e+01 ... (remaining 3895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 3217 1.63 - 3.25: 1000 3.25 - 4.88: 806 4.88 - 6.50: 149 6.50 - 8.13: 12 Bond angle restraints: 5184 Sorted by residual: angle pdb=" CA GLY A 291 " pdb=" C GLY A 291 " pdb=" O GLY A 291 " ideal model delta sigma weight residual 122.23 117.52 4.71 6.90e-01 2.10e+00 4.67e+01 angle pdb=" CA GLY I 291 " pdb=" C GLY I 291 " pdb=" O GLY I 291 " ideal model delta sigma weight residual 122.23 117.54 4.69 6.90e-01 2.10e+00 4.62e+01 angle pdb=" CA GLY C 291 " pdb=" C GLY C 291 " pdb=" O GLY C 291 " ideal model delta sigma weight residual 122.23 117.55 4.68 6.90e-01 2.10e+00 4.60e+01 angle pdb=" CA GLY G 291 " pdb=" C GLY G 291 " pdb=" O GLY G 291 " ideal model delta sigma weight residual 122.23 117.56 4.67 6.90e-01 2.10e+00 4.58e+01 angle pdb=" CA GLY K 291 " pdb=" C GLY K 291 " pdb=" O GLY K 291 " ideal model delta sigma weight residual 122.23 117.56 4.67 6.90e-01 2.10e+00 4.58e+01 ... (remaining 5179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.96: 1779 14.96 - 29.91: 177 29.91 - 44.86: 12 44.86 - 59.82: 24 59.82 - 74.77: 24 Dihedral angle restraints: 2016 sinusoidal: 744 harmonic: 1272 Sorted by residual: dihedral pdb=" CA ASN J 268 " pdb=" CB ASN J 268 " pdb=" CG ASN J 268 " pdb=" OD1 ASN J 268 " ideal model delta sinusoidal sigma weight residual -90.00 -160.75 70.75 2 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASN F 268 " pdb=" CB ASN F 268 " pdb=" CG ASN F 268 " pdb=" OD1 ASN F 268 " ideal model delta sinusoidal sigma weight residual -90.00 -160.74 70.74 2 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASN L 268 " pdb=" CB ASN L 268 " pdb=" CG ASN L 268 " pdb=" OD1 ASN L 268 " ideal model delta sinusoidal sigma weight residual -90.00 -160.74 70.74 2 2.00e+01 2.50e-03 1.07e+01 ... (remaining 2013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 120 0.034 - 0.068: 96 0.068 - 0.102: 48 0.102 - 0.136: 36 0.136 - 0.170: 48 Chirality restraints: 348 Sorted by residual: chirality pdb=" CA TYR F 260 " pdb=" N TYR F 260 " pdb=" C TYR F 260 " pdb=" CB TYR F 260 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA TYR J 260 " pdb=" N TYR J 260 " pdb=" C TYR J 260 " pdb=" CB TYR J 260 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA TYR H 260 " pdb=" N TYR H 260 " pdb=" C TYR H 260 " pdb=" CB TYR H 260 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.14e-01 ... (remaining 345 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER J 270 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C SER J 270 " -0.058 2.00e-02 2.50e+03 pdb=" O SER J 270 " 0.022 2.00e-02 2.50e+03 pdb=" N SER J 271 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 270 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C SER E 270 " 0.058 2.00e-02 2.50e+03 pdb=" O SER E 270 " -0.022 2.00e-02 2.50e+03 pdb=" N SER E 271 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 270 " 0.016 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C SER L 270 " -0.058 2.00e-02 2.50e+03 pdb=" O SER L 270 " 0.022 2.00e-02 2.50e+03 pdb=" N SER L 271 " 0.020 2.00e-02 2.50e+03 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 2390 3.02 - 3.49: 3846 3.49 - 3.96: 6869 3.96 - 4.43: 7785 4.43 - 4.90: 15100 Nonbonded interactions: 35990 Sorted by model distance: nonbonded pdb=" N SER F 286 " pdb=" O SER F 286 " model vdw 2.548 2.496 nonbonded pdb=" N SER L 286 " pdb=" O SER L 286 " model vdw 2.548 2.496 nonbonded pdb=" N SER D 286 " pdb=" O SER D 286 " model vdw 2.548 2.496 nonbonded pdb=" N SER B 286 " pdb=" O SER B 286 " model vdw 2.548 2.496 nonbonded pdb=" N SER H 286 " pdb=" O SER H 286 " model vdw 2.548 2.496 ... (remaining 35985 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.290 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 0.014 0.054 3900 Z= 1.050 Angle : 2.210 8.127 5184 Z= 1.661 Chirality : 0.082 0.170 348 Planarity : 0.011 0.034 780 Dihedral : 15.288 74.770 1320 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 24.14 % Favored : 75.86 % 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: -3.75 (0.24), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.18), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 284 TYR 0.029 0.004 TYR D 260 PHE 0.012 0.004 PHE F 273 Details of bonding type rmsd covalent geometry : bond 0.01409 ( 3900) covalent geometry : angle 2.20994 ( 5184) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 263 PHE cc_start: 0.8219 (p90) cc_final: 0.7186 (m-80) REVERT: A 284 ARG cc_start: 0.8298 (ttt180) cc_final: 0.6212 (mtm-85) REVERT: A 289 TYR cc_start: 0.8717 (m-80) cc_final: 0.6974 (p90) REVERT: B 263 PHE cc_start: 0.8106 (p90) cc_final: 0.7126 (m-80) REVERT: B 266 TYR cc_start: 0.8254 (m-80) cc_final: 0.7807 (m-80) REVERT: B 284 ARG cc_start: 0.8026 (ttt180) cc_final: 0.5420 (mpt180) REVERT: B 289 TYR cc_start: 0.8639 (m-80) cc_final: 0.6974 (p90) REVERT: C 252 SER cc_start: 0.8580 (m) cc_final: 0.8241 (m) REVERT: C 266 TYR cc_start: 0.8269 (m-80) cc_final: 0.8007 (m-80) REVERT: G 266 TYR cc_start: 0.8346 (m-80) cc_final: 0.8126 (m-80) REVERT: H 266 TYR cc_start: 0.8347 (m-80) cc_final: 0.8106 (m-80) REVERT: J 263 PHE cc_start: 0.8410 (p90) cc_final: 0.8188 (p90) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.0693 time to fit residues: 20.3882 Evaluate side-chains 180 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.145168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.133709 restraints weight = 6634.184| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 2.99 r_work: 0.4157 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3900 Z= 0.146 Angle : 0.568 4.627 5184 Z= 0.329 Chirality : 0.030 0.078 348 Planarity : 0.004 0.021 780 Dihedral : 4.392 10.775 588 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.03 % Allowed : 23.28 % Favored : 70.69 % 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: -3.65 (0.25), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.19), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 284 TYR 0.023 0.002 TYR I 260 PHE 0.027 0.002 PHE C 263 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 3900) covalent geometry : angle 0.56791 ( 5184) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 263 PHE cc_start: 0.8746 (p90) cc_final: 0.6887 (m-10) REVERT: A 284 ARG cc_start: 0.8688 (ttt180) cc_final: 0.5420 (mtt90) REVERT: A 289 TYR cc_start: 0.9073 (m-80) cc_final: 0.6981 (p90) REVERT: B 263 PHE cc_start: 0.8885 (p90) cc_final: 0.6738 (m-80) REVERT: B 266 TYR cc_start: 0.8715 (m-80) cc_final: 0.7931 (m-80) REVERT: B 289 TYR cc_start: 0.8855 (m-80) cc_final: 0.6913 (p90) REVERT: C 252 SER cc_start: 0.8379 (m) cc_final: 0.8065 (m) REVERT: C 260 TYR cc_start: 0.8262 (t80) cc_final: 0.8047 (t80) REVERT: C 263 PHE cc_start: 0.9116 (p90) cc_final: 0.8703 (p90) REVERT: D 276 MET cc_start: 0.9460 (ttp) cc_final: 0.9117 (tmm) REVERT: E 266 TYR cc_start: 0.9342 (m-80) cc_final: 0.8818 (m-80) REVERT: F 272 ASN cc_start: 0.8110 (t0) cc_final: 0.7908 (t0) REVERT: F 276 MET cc_start: 0.9245 (ttp) cc_final: 0.8814 (ttt) REVERT: I 263 PHE cc_start: 0.9100 (p90) cc_final: 0.8549 (p90) REVERT: J 252 SER cc_start: 0.8318 (m) cc_final: 0.7770 (m) REVERT: J 263 PHE cc_start: 0.9172 (p90) cc_final: 0.8916 (p90) REVERT: J 266 TYR cc_start: 0.9271 (m-80) cc_final: 0.8946 (m-80) REVERT: J 272 ASN cc_start: 0.7907 (t0) cc_final: 0.7272 (t0) REVERT: J 276 MET cc_start: 0.9005 (ttp) cc_final: 0.8049 (ttp) REVERT: K 260 TYR cc_start: 0.8481 (t80) cc_final: 0.8250 (t80) REVERT: K 280 ASN cc_start: 0.7846 (p0) cc_final: 0.7046 (t0) REVERT: L 266 TYR cc_start: 0.9063 (m-80) cc_final: 0.8761 (m-80) REVERT: L 272 ASN cc_start: 0.6689 (t0) cc_final: 0.6217 (p0) REVERT: L 280 ASN cc_start: 0.8231 (p0) cc_final: 0.6761 (m-40) REVERT: L 281 PHE cc_start: 0.7478 (m-80) cc_final: 0.6963 (m-80) REVERT: L 289 TYR cc_start: 0.8659 (m-80) cc_final: 0.8454 (m-80) outliers start: 21 outliers final: 15 residues processed: 168 average time/residue: 0.0548 time to fit residues: 11.8876 Evaluate side-chains 161 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 270 SER Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain L residue 252 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 0.0770 chunk 40 optimal weight: 3.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 ASN E 265 ASN I 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.142938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.130909 restraints weight = 6544.643| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.96 r_work: 0.4122 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3900 Z= 0.191 Angle : 0.518 4.010 5184 Z= 0.300 Chirality : 0.030 0.076 348 Planarity : 0.003 0.022 780 Dihedral : 4.438 10.844 588 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.05 % Allowed : 23.28 % Favored : 68.68 % 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: -3.60 (0.24), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.18), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 284 TYR 0.018 0.002 TYR A 260 PHE 0.045 0.003 PHE L 263 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 3900) covalent geometry : angle 0.51779 ( 5184) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.094 Fit side-chains REVERT: A 289 TYR cc_start: 0.9039 (m-80) cc_final: 0.7063 (p90) REVERT: A 295 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: B 259 SER cc_start: 0.7220 (OUTLIER) cc_final: 0.6294 (p) REVERT: B 266 TYR cc_start: 0.8867 (m-80) cc_final: 0.8500 (m-80) REVERT: B 276 MET cc_start: 0.8080 (ttp) cc_final: 0.7780 (mtt) REVERT: C 260 TYR cc_start: 0.8296 (t80) cc_final: 0.7992 (t80) REVERT: C 261 ASN cc_start: 0.9338 (m-40) cc_final: 0.9113 (m-40) REVERT: C 263 PHE cc_start: 0.9279 (p90) cc_final: 0.8991 (p90) REVERT: D 260 TYR cc_start: 0.8491 (t80) cc_final: 0.8272 (t80) REVERT: D 276 MET cc_start: 0.9460 (ttp) cc_final: 0.8770 (tmm) REVERT: F 259 SER cc_start: 0.8920 (OUTLIER) cc_final: 0.8372 (p) REVERT: F 276 MET cc_start: 0.9462 (ttp) cc_final: 0.8183 (ttp) REVERT: F 295 TYR cc_start: 0.7382 (OUTLIER) cc_final: 0.6836 (m-80) REVERT: G 263 PHE cc_start: 0.9215 (p90) cc_final: 0.8944 (p90) REVERT: G 276 MET cc_start: 0.9493 (ttp) cc_final: 0.8795 (tmm) REVERT: H 263 PHE cc_start: 0.9179 (p90) cc_final: 0.8400 (p90) REVERT: H 266 TYR cc_start: 0.9314 (m-80) cc_final: 0.9066 (m-80) REVERT: I 272 ASN cc_start: 0.8460 (t0) cc_final: 0.7867 (t0) REVERT: I 276 MET cc_start: 0.8655 (ttp) cc_final: 0.8155 (ppp) REVERT: J 252 SER cc_start: 0.8463 (m) cc_final: 0.8199 (p) REVERT: J 261 ASN cc_start: 0.9376 (m-40) cc_final: 0.8998 (m-40) REVERT: J 266 TYR cc_start: 0.9044 (m-80) cc_final: 0.8735 (m-80) REVERT: J 272 ASN cc_start: 0.8019 (t0) cc_final: 0.7699 (t0) REVERT: K 272 ASN cc_start: 0.6407 (t0) cc_final: 0.6034 (p0) REVERT: K 280 ASN cc_start: 0.8061 (p0) cc_final: 0.6681 (t0) REVERT: K 281 PHE cc_start: 0.8199 (m-80) cc_final: 0.7873 (m-80) REVERT: L 272 ASN cc_start: 0.6868 (t0) cc_final: 0.6509 (p0) REVERT: L 276 MET cc_start: 0.8364 (ttp) cc_final: 0.7870 (ppp) outliers start: 28 outliers final: 21 residues processed: 155 average time/residue: 0.0491 time to fit residues: 9.9227 Evaluate side-chains 163 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 295 TYR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 270 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 0.0050 chunk 43 optimal weight: 0.1980 chunk 15 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 ASN L 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.144677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.133910 restraints weight = 6523.793| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 2.86 r_work: 0.4202 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3900 Z= 0.126 Angle : 0.474 3.499 5184 Z= 0.273 Chirality : 0.029 0.077 348 Planarity : 0.003 0.020 780 Dihedral : 3.932 10.574 588 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 8.33 % Allowed : 24.14 % Favored : 67.53 % 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: -3.56 (0.23), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 284 TYR 0.021 0.002 TYR C 266 PHE 0.028 0.002 PHE F 281 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 3900) covalent geometry : angle 0.47446 ( 5184) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.127 Fit side-chains REVERT: A 289 TYR cc_start: 0.9058 (m-80) cc_final: 0.7085 (p90) REVERT: A 295 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.7373 (m-80) REVERT: B 259 SER cc_start: 0.7211 (OUTLIER) cc_final: 0.6282 (p) REVERT: B 276 MET cc_start: 0.8001 (ttp) cc_final: 0.7758 (mtt) REVERT: C 263 PHE cc_start: 0.9213 (p90) cc_final: 0.8920 (p90) REVERT: C 266 TYR cc_start: 0.9328 (m-80) cc_final: 0.9034 (m-80) REVERT: D 263 PHE cc_start: 0.9113 (p90) cc_final: 0.8890 (p90) REVERT: D 276 MET cc_start: 0.9481 (ttp) cc_final: 0.8746 (tmm) REVERT: F 259 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8383 (p) REVERT: F 276 MET cc_start: 0.9404 (ttp) cc_final: 0.8585 (ttp) REVERT: F 295 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.6950 (m-80) REVERT: G 259 SER cc_start: 0.8938 (OUTLIER) cc_final: 0.8413 (p) REVERT: G 276 MET cc_start: 0.9468 (ttp) cc_final: 0.8728 (tmm) REVERT: H 266 TYR cc_start: 0.9295 (m-80) cc_final: 0.9066 (m-80) REVERT: I 266 TYR cc_start: 0.9222 (m-80) cc_final: 0.8907 (m-80) REVERT: I 272 ASN cc_start: 0.8275 (t0) cc_final: 0.7768 (t0) REVERT: I 276 MET cc_start: 0.9097 (ttp) cc_final: 0.8767 (ttp) REVERT: J 252 SER cc_start: 0.8377 (m) cc_final: 0.8135 (p) REVERT: J 261 ASN cc_start: 0.9226 (m-40) cc_final: 0.8907 (m-40) REVERT: J 266 TYR cc_start: 0.9118 (m-80) cc_final: 0.8688 (m-80) REVERT: J 272 ASN cc_start: 0.8190 (t0) cc_final: 0.7620 (t0) REVERT: K 260 TYR cc_start: 0.8590 (t80) cc_final: 0.8314 (t80) REVERT: K 272 ASN cc_start: 0.6269 (t0) cc_final: 0.6030 (p0) REVERT: K 276 MET cc_start: 0.8420 (ttp) cc_final: 0.8173 (ttp) REVERT: L 260 TYR cc_start: 0.8636 (t80) cc_final: 0.8418 (t80) REVERT: L 272 ASN cc_start: 0.6591 (t0) cc_final: 0.6345 (p0) REVERT: L 280 ASN cc_start: 0.7216 (p0) cc_final: 0.6264 (t0) outliers start: 29 outliers final: 19 residues processed: 155 average time/residue: 0.0561 time to fit residues: 11.0640 Evaluate side-chains 159 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 295 TYR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 295 TYR Chi-restraints excluded: chain L residue 252 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 27 optimal weight: 5.9990 chunk 7 optimal weight: 0.0980 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN D 261 ASN ** F 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.144242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.133316 restraints weight = 6540.363| |-----------------------------------------------------------------------------| r_work (start): 0.4284 rms_B_bonded: 2.80 r_work: 0.4201 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3900 Z= 0.151 Angle : 0.474 3.433 5184 Z= 0.271 Chirality : 0.029 0.089 348 Planarity : 0.003 0.023 780 Dihedral : 3.869 10.959 588 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 7.76 % Allowed : 22.99 % Favored : 69.25 % 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: -3.53 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 284 TYR 0.027 0.002 TYR C 266 PHE 0.024 0.003 PHE F 281 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 3900) covalent geometry : angle 0.47355 ( 5184) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.134 Fit side-chains REVERT: A 289 TYR cc_start: 0.9038 (m-80) cc_final: 0.7040 (p90) REVERT: A 295 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.7502 (m-80) REVERT: B 259 SER cc_start: 0.7149 (OUTLIER) cc_final: 0.6474 (p) REVERT: C 260 TYR cc_start: 0.8368 (t80) cc_final: 0.8157 (t80) REVERT: C 263 PHE cc_start: 0.9238 (p90) cc_final: 0.8919 (p90) REVERT: C 266 TYR cc_start: 0.9271 (m-80) cc_final: 0.8802 (m-80) REVERT: C 295 TYR cc_start: 0.7537 (OUTLIER) cc_final: 0.7149 (m-80) REVERT: D 276 MET cc_start: 0.9471 (ttp) cc_final: 0.9025 (tmm) REVERT: E 259 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8310 (p) REVERT: F 276 MET cc_start: 0.9377 (ttp) cc_final: 0.8377 (ttp) REVERT: F 295 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.6816 (m-80) REVERT: H 266 TYR cc_start: 0.9386 (m-80) cc_final: 0.8966 (m-80) REVERT: I 266 TYR cc_start: 0.9228 (m-80) cc_final: 0.8921 (m-80) REVERT: I 272 ASN cc_start: 0.8122 (t0) cc_final: 0.7440 (t0) REVERT: I 276 MET cc_start: 0.9090 (ttp) cc_final: 0.8737 (ttp) REVERT: J 252 SER cc_start: 0.8395 (m) cc_final: 0.8139 (p) REVERT: J 261 ASN cc_start: 0.9195 (m-40) cc_final: 0.8899 (m-40) REVERT: J 266 TYR cc_start: 0.9274 (m-80) cc_final: 0.8755 (m-80) REVERT: J 272 ASN cc_start: 0.7991 (t0) cc_final: 0.7709 (t0) REVERT: K 260 TYR cc_start: 0.8566 (t80) cc_final: 0.8303 (t80) REVERT: K 272 ASN cc_start: 0.6336 (t0) cc_final: 0.6112 (p0) REVERT: K 276 MET cc_start: 0.8569 (ttp) cc_final: 0.8287 (ttp) REVERT: L 280 ASN cc_start: 0.7287 (p0) cc_final: 0.6279 (t0) REVERT: L 295 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.7257 (m-80) outliers start: 27 outliers final: 20 residues processed: 145 average time/residue: 0.0544 time to fit residues: 10.2461 Evaluate side-chains 154 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 295 TYR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 295 TYR Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 295 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 19 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN ** L 265 ASN ** 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 = 0.4217 r_free = 0.4217 target = 0.130334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.119156 restraints weight = 7194.697| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 2.78 r_work: 0.3993 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 3900 Z= 0.343 Angle : 0.567 3.611 5184 Z= 0.323 Chirality : 0.031 0.099 348 Planarity : 0.003 0.025 780 Dihedral : 4.643 12.747 588 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 10.06 % Allowed : 19.25 % Favored : 70.69 % 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: -3.55 (0.21), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.16), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 284 TYR 0.021 0.002 TYR D 260 PHE 0.029 0.004 PHE F 273 Details of bonding type rmsd covalent geometry : bond 0.00747 ( 3900) covalent geometry : angle 0.56715 ( 5184) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.154 Fit side-chains REVERT: A 289 TYR cc_start: 0.8988 (m-80) cc_final: 0.6904 (p90) REVERT: A 295 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7751 (m-80) REVERT: C 295 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: D 262 ASP cc_start: 0.8846 (t0) cc_final: 0.8628 (t0) REVERT: D 284 ARG cc_start: 0.9295 (OUTLIER) cc_final: 0.8507 (ttm170) REVERT: E 259 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8400 (p) REVERT: F 276 MET cc_start: 0.9404 (ttp) cc_final: 0.8289 (ttp) REVERT: F 295 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.6875 (m-80) REVERT: H 262 ASP cc_start: 0.8862 (t0) cc_final: 0.8648 (t0) REVERT: I 272 ASN cc_start: 0.8406 (t0) cc_final: 0.7732 (t0) REVERT: I 276 MET cc_start: 0.9067 (ttp) cc_final: 0.8674 (ttp) REVERT: J 252 SER cc_start: 0.8530 (m) cc_final: 0.8192 (p) REVERT: J 261 ASN cc_start: 0.9286 (m-40) cc_final: 0.8957 (m-40) REVERT: J 266 TYR cc_start: 0.9425 (m-80) cc_final: 0.8960 (m-80) REVERT: K 272 ASN cc_start: 0.6331 (t0) cc_final: 0.6102 (p0) REVERT: L 263 PHE cc_start: 0.7457 (p90) cc_final: 0.7216 (p90) REVERT: L 272 ASN cc_start: 0.8171 (p0) cc_final: 0.7262 (m-40) REVERT: L 295 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.7327 (m-80) outliers start: 35 outliers final: 20 residues processed: 141 average time/residue: 0.0473 time to fit residues: 8.5940 Evaluate side-chains 146 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 284 ARG Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 295 TYR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 295 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN C 261 ASN ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.138175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.126284 restraints weight = 7136.998| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 2.91 r_work: 0.4096 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 3900 Z= 0.168 Angle : 0.485 3.289 5184 Z= 0.277 Chirality : 0.030 0.087 348 Planarity : 0.003 0.023 780 Dihedral : 4.057 12.660 588 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 9.20 % Allowed : 21.26 % Favored : 69.54 % 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: -3.54 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 284 TYR 0.018 0.002 TYR D 260 PHE 0.026 0.003 PHE D 263 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3900) covalent geometry : angle 0.48525 ( 5184) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.134 Fit side-chains REVERT: A 289 TYR cc_start: 0.9048 (m-80) cc_final: 0.7021 (p90) REVERT: A 295 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7622 (m-80) REVERT: B 289 TYR cc_start: 0.8846 (m-80) cc_final: 0.6910 (p90) REVERT: C 263 PHE cc_start: 0.9265 (p90) cc_final: 0.8995 (p90) REVERT: C 295 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.7409 (m-80) REVERT: D 276 MET cc_start: 0.9412 (ttp) cc_final: 0.8984 (tmm) REVERT: E 259 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8349 (p) REVERT: E 272 ASN cc_start: 0.8405 (t0) cc_final: 0.8197 (t0) REVERT: F 276 MET cc_start: 0.9410 (ttp) cc_final: 0.8218 (ttp) REVERT: F 295 TYR cc_start: 0.7870 (OUTLIER) cc_final: 0.7252 (m-80) REVERT: G 276 MET cc_start: 0.9435 (ttp) cc_final: 0.8631 (tmm) REVERT: H 262 ASP cc_start: 0.8764 (t0) cc_final: 0.8545 (t0) REVERT: H 266 TYR cc_start: 0.9411 (m-80) cc_final: 0.9061 (m-80) REVERT: I 272 ASN cc_start: 0.8160 (t0) cc_final: 0.7552 (t0) REVERT: I 276 MET cc_start: 0.9059 (ttp) cc_final: 0.8243 (tmm) REVERT: J 252 SER cc_start: 0.8391 (m) cc_final: 0.8047 (p) REVERT: J 261 ASN cc_start: 0.9117 (m-40) cc_final: 0.8860 (m-40) REVERT: J 266 TYR cc_start: 0.9361 (m-80) cc_final: 0.8833 (m-80) REVERT: K 266 TYR cc_start: 0.9049 (m-80) cc_final: 0.8774 (m-80) REVERT: L 272 ASN cc_start: 0.8312 (p0) cc_final: 0.7092 (m-40) REVERT: L 295 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.7332 (m-80) outliers start: 32 outliers final: 23 residues processed: 144 average time/residue: 0.0500 time to fit residues: 9.3420 Evaluate side-chains 151 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 295 TYR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 295 TYR Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 295 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 ASN ** L 265 ASN ** 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 = 0.4215 r_free = 0.4215 target = 0.131107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.119382 restraints weight = 7226.975| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.91 r_work: 0.3987 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.028 3900 Z= 0.303 Angle : 0.544 3.766 5184 Z= 0.310 Chirality : 0.031 0.089 348 Planarity : 0.003 0.023 780 Dihedral : 4.521 12.654 588 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 8.62 % Allowed : 20.69 % Favored : 70.69 % 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: -3.55 (0.22), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 284 TYR 0.031 0.002 TYR E 266 PHE 0.027 0.003 PHE F 281 Details of bonding type rmsd covalent geometry : bond 0.00654 ( 3900) covalent geometry : angle 0.54445 ( 5184) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.139 Fit side-chains REVERT: A 289 TYR cc_start: 0.9002 (m-80) cc_final: 0.6915 (p90) REVERT: A 295 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7700 (m-80) REVERT: C 295 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.7299 (m-80) REVERT: D 263 PHE cc_start: 0.9171 (p90) cc_final: 0.8831 (p90) REVERT: E 259 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8473 (p) REVERT: F 276 MET cc_start: 0.9423 (ttp) cc_final: 0.8308 (ttp) REVERT: F 295 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.7248 (m-80) REVERT: G 276 MET cc_start: 0.9470 (ttp) cc_final: 0.8585 (tmm) REVERT: H 262 ASP cc_start: 0.8897 (t0) cc_final: 0.8632 (t0) REVERT: I 276 MET cc_start: 0.9093 (ttp) cc_final: 0.8276 (tmm) REVERT: J 261 ASN cc_start: 0.9279 (m-40) cc_final: 0.8980 (m-40) REVERT: J 266 TYR cc_start: 0.9431 (m-80) cc_final: 0.8887 (m-80) REVERT: K 266 TYR cc_start: 0.9070 (m-80) cc_final: 0.8855 (m-80) REVERT: K 272 ASN cc_start: 0.8319 (p0) cc_final: 0.7648 (t0) REVERT: L 295 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.7363 (m-80) outliers start: 30 outliers final: 22 residues processed: 131 average time/residue: 0.0590 time to fit residues: 9.8752 Evaluate side-chains 137 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 295 TYR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain K residue 295 TYR Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 295 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 8 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.0770 chunk 45 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.141298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.129796 restraints weight = 6666.619| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.90 r_work: 0.4166 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.6222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3900 Z= 0.123 Angle : 0.478 3.619 5184 Z= 0.276 Chirality : 0.031 0.093 348 Planarity : 0.003 0.025 780 Dihedral : 3.832 14.240 588 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 6.90 % Allowed : 22.41 % Favored : 70.69 % 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: -3.50 (0.23), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 284 TYR 0.020 0.001 TYR D 260 PHE 0.024 0.002 PHE F 281 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 3900) covalent geometry : angle 0.47788 ( 5184) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.109 Fit side-chains REVERT: A 284 ARG cc_start: 0.8357 (ttt180) cc_final: 0.4753 (mpt180) REVERT: A 289 TYR cc_start: 0.9030 (m-80) cc_final: 0.6892 (p90) REVERT: A 295 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7564 (m-80) REVERT: B 259 SER cc_start: 0.7051 (OUTLIER) cc_final: 0.6101 (p) REVERT: B 266 TYR cc_start: 0.7380 (m-10) cc_final: 0.4356 (p90) REVERT: B 289 TYR cc_start: 0.8800 (m-80) cc_final: 0.6863 (p90) REVERT: C 260 TYR cc_start: 0.8409 (t80) cc_final: 0.8172 (t80) REVERT: C 263 PHE cc_start: 0.9317 (p90) cc_final: 0.9117 (p90) REVERT: D 276 MET cc_start: 0.9423 (ttp) cc_final: 0.8969 (tmm) REVERT: F 276 MET cc_start: 0.9358 (ttp) cc_final: 0.8212 (ttp) REVERT: F 295 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7752 (m-80) REVERT: G 252 SER cc_start: 0.8531 (OUTLIER) cc_final: 0.8231 (p) REVERT: H 262 ASP cc_start: 0.8694 (t0) cc_final: 0.8436 (t0) REVERT: I 276 MET cc_start: 0.9137 (ttp) cc_final: 0.8158 (tmm) REVERT: J 266 TYR cc_start: 0.9367 (m-80) cc_final: 0.9047 (m-80) REVERT: K 260 TYR cc_start: 0.8636 (t80) cc_final: 0.8354 (t80) REVERT: K 266 TYR cc_start: 0.8934 (m-80) cc_final: 0.8559 (m-80) REVERT: K 280 ASN cc_start: 0.7168 (p0) cc_final: 0.5908 (t0) REVERT: K 281 PHE cc_start: 0.6758 (m-80) cc_final: 0.6503 (m-80) REVERT: L 280 ASN cc_start: 0.6323 (p0) cc_final: 0.5681 (t0) REVERT: L 295 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.7344 (m-80) outliers start: 24 outliers final: 18 residues processed: 136 average time/residue: 0.0559 time to fit residues: 9.8310 Evaluate side-chains 142 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 295 TYR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 295 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 261 ASN ** J 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 265 ASN ** 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 = 0.4336 r_free = 0.4336 target = 0.139776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.127520 restraints weight = 7028.145| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 3.00 r_work: 0.4115 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.6156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3900 Z= 0.173 Angle : 0.492 3.695 5184 Z= 0.285 Chirality : 0.031 0.102 348 Planarity : 0.003 0.021 780 Dihedral : 3.909 12.774 588 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 6.90 % Allowed : 22.99 % Favored : 70.11 % 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: -3.50 (0.23), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.17), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 284 TYR 0.019 0.002 TYR D 260 PHE 0.025 0.002 PHE D 263 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 3900) covalent geometry : angle 0.49220 ( 5184) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.134 Fit side-chains REVERT: A 289 TYR cc_start: 0.9041 (m-80) cc_final: 0.6961 (p90) REVERT: A 295 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7603 (m-80) REVERT: B 259 SER cc_start: 0.7092 (OUTLIER) cc_final: 0.6115 (p) REVERT: B 289 TYR cc_start: 0.8811 (m-80) cc_final: 0.6888 (p90) REVERT: D 263 PHE cc_start: 0.9012 (p90) cc_final: 0.8759 (p90) REVERT: D 276 MET cc_start: 0.9362 (ttp) cc_final: 0.8897 (tmm) REVERT: F 276 MET cc_start: 0.9361 (ttp) cc_final: 0.8128 (ttp) REVERT: F 295 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7741 (m-80) REVERT: G 263 PHE cc_start: 0.9093 (p90) cc_final: 0.8869 (p90) REVERT: H 262 ASP cc_start: 0.8748 (t0) cc_final: 0.8474 (t0) REVERT: H 272 ASN cc_start: 0.9174 (t0) cc_final: 0.8783 (t0) REVERT: I 276 MET cc_start: 0.9148 (ttp) cc_final: 0.8699 (ttp) REVERT: I 281 PHE cc_start: 0.8798 (m-80) cc_final: 0.8584 (m-80) REVERT: J 266 TYR cc_start: 0.9404 (m-80) cc_final: 0.9080 (m-80) REVERT: K 266 TYR cc_start: 0.8944 (m-80) cc_final: 0.8701 (m-80) REVERT: K 280 ASN cc_start: 0.7242 (p0) cc_final: 0.5875 (t0) REVERT: L 280 ASN cc_start: 0.6847 (p0) cc_final: 0.5636 (t0) REVERT: L 295 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.7325 (m-80) outliers start: 24 outliers final: 19 residues processed: 124 average time/residue: 0.0501 time to fit residues: 8.2081 Evaluate side-chains 135 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 285 SER Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 295 TYR Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 295 TYR Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain H residue 252 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain I residue 252 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 285 SER Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 270 SER Chi-restraints excluded: chain L residue 252 SER Chi-restraints excluded: chain L residue 295 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.0070 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 0.0970 chunk 4 optimal weight: 0.0870 chunk 24 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.153252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.140501 restraints weight = 6595.362| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 3.13 r_work: 0.4300 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.6494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3900 Z= 0.102 Angle : 0.469 3.818 5184 Z= 0.273 Chirality : 0.032 0.101 348 Planarity : 0.003 0.019 780 Dihedral : 3.481 12.242 588 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 5.46 % Allowed : 24.43 % Favored : 70.11 % 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: -3.47 (0.23), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.18), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 284 TYR 0.027 0.001 TYR G 266 PHE 0.024 0.002 PHE D 263 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 3900) covalent geometry : angle 0.46869 ( 5184) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 988.80 seconds wall clock time: 17 minutes 33.20 seconds (1053.20 seconds total)