Starting phenix.real_space_refine on Tue Aug 4 12:38:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25if_80132/08_2026/25if_80132.cif Found real_map, /net/cci-nas-00/data/ceres_data/25if_80132/08_2026/25if_80132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25if_80132/08_2026/25if_80132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25if_80132/08_2026/25if_80132.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25if_80132/08_2026/25if_80132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25if_80132/08_2026/25if_80132.map" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 22 5.16 5 C 1842 2.51 5 N 488 2.21 5 O 464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2816 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2221 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 270} Chain: "B" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 595 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 69} Time building chain proxies: 1.07, per 1000 atoms: 0.38 Number of scatterers: 2816 At special positions: 0 Unit cell: (54.6564, 104.758, 61.9439, 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 22 16.00 O 464 8.00 N 488 7.00 C 1842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 50 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 57 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 58 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 135.5 milliseconds 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 670 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 1 sheets defined 79.8% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 39 through 68 Proline residue: A 57 - end of helix Processing helix chain 'A' and resid 75 through 92 removed outlier: 4.417A pdb=" N PHE A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 102 removed outlier: 3.712A pdb=" N LEU A 96 " --> pdb=" O SER A 92 " (cutoff:3.500A) Proline residue: A 99 - end of helix Processing helix chain 'A' and resid 108 through 144 removed outlier: 4.137A pdb=" N GLY A 112 " --> pdb=" O TYR A 108 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TRP A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER A 117 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 148 removed outlier: 3.804A pdb=" N LYS A 148 " --> pdb=" O PRO A 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 145 through 148' Processing helix chain 'A' and resid 151 through 178 removed outlier: 3.871A pdb=" N PHE A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A) Proline residue: A 174 - end of helix Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 215 through 233 removed outlier: 3.504A pdb=" N LEU A 219 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 263 removed outlier: 3.557A pdb=" N THR A 242 " --> pdb=" O TRP A 238 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA A 243 " --> pdb=" O PRO A 239 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Proline residue: A 254 - end of helix Processing helix chain 'A' and resid 269 through 277 Processing helix chain 'A' and resid 278 through 288 removed outlier: 3.835A pdb=" N PHE A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 300 removed outlier: 3.764A pdb=" N ASN A 293 " --> pdb=" O HIS A 289 " (cutoff:3.500A) Proline residue: A 294 - end of helix removed outlier: 3.516A pdb=" N PHE A 300 " --> pdb=" O MET A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'B' and resid 4 through 15 Processing helix chain 'B' and resid 18 through 29 removed outlier: 3.713A pdb=" N LYS B 22 " --> pdb=" O HIS B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 43 removed outlier: 3.536A pdb=" N ARG B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 67 removed outlier: 4.212A pdb=" N GLU B 67 " --> pdb=" O LYS B 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 182 through 184 removed outlier: 3.770A pdb=" N ARG A 189 " --> pdb=" O GLU A 184 " (cutoff:3.500A) 189 hydrogen bonds defined for protein. 564 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.41 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 879 1.35 - 1.46: 717 1.46 - 1.58: 1271 1.58 - 1.70: 0 1.70 - 1.82: 28 Bond restraints: 2895 Sorted by residual: bond pdb=" N HIS B 3 " pdb=" CA HIS B 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N VAL A 27 " pdb=" CA VAL A 27 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.63e+00 bond pdb=" CA ASP A 28 " pdb=" C ASP A 28 " ideal model delta sigma weight residual 1.532 1.523 0.010 9.60e-03 1.09e+04 1.01e+00 bond pdb=" C PRO B 48 " pdb=" O PRO B 48 " ideal model delta sigma weight residual 1.237 1.248 -0.010 1.26e-02 6.30e+03 6.94e-01 bond pdb=" C LYS B 71 " pdb=" N PRO B 72 " ideal model delta sigma weight residual 1.333 1.342 -0.008 1.01e-02 9.80e+03 6.61e-01 ... (remaining 2890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 3767 1.10 - 2.21: 140 2.21 - 3.31: 21 3.31 - 4.41: 13 4.41 - 5.51: 2 Bond angle restraints: 3943 Sorted by residual: angle pdb=" CB ARG B 52 " pdb=" CG ARG B 52 " pdb=" CD ARG B 52 " ideal model delta sigma weight residual 111.30 116.81 -5.51 2.30e+00 1.89e-01 5.75e+00 angle pdb=" CA SER A 92 " pdb=" C SER A 92 " pdb=" N LEU A 93 " ideal model delta sigma weight residual 118.27 122.07 -3.80 1.59e+00 3.96e-01 5.70e+00 angle pdb=" C CYS A 251 " pdb=" N TRP A 252 " pdb=" CA TRP A 252 " ideal model delta sigma weight residual 122.29 119.42 2.87 1.56e+00 4.11e-01 3.38e+00 angle pdb=" CA VAL A 39 " pdb=" C VAL A 39 " pdb=" O VAL A 39 " ideal model delta sigma weight residual 119.29 120.81 -1.52 8.40e-01 1.42e+00 3.30e+00 angle pdb=" N VAL A 39 " pdb=" CA VAL A 39 " pdb=" C VAL A 39 " ideal model delta sigma weight residual 112.96 111.16 1.80 1.00e+00 1.00e+00 3.25e+00 ... (remaining 3938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.60: 1517 15.60 - 31.21: 147 31.21 - 46.81: 35 46.81 - 62.41: 2 62.41 - 78.02: 3 Dihedral angle restraints: 1704 sinusoidal: 663 harmonic: 1041 Sorted by residual: dihedral pdb=" CB CYS B 25 " pdb=" SG CYS B 25 " pdb=" SG CYS B 57 " pdb=" CB CYS B 57 " ideal model delta sinusoidal sigma weight residual -86.00 -115.05 29.05 1 1.00e+01 1.00e-02 1.21e+01 dihedral pdb=" CA ASP A 38 " pdb=" C ASP A 38 " pdb=" N VAL A 39 " pdb=" CA VAL A 39 " ideal model delta harmonic sigma weight residual 180.00 -163.05 -16.95 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA CYS A 29 " pdb=" C CYS A 29 " pdb=" N PRO A 30 " pdb=" CA PRO A 30 " ideal model delta harmonic sigma weight residual -180.00 -163.43 -16.57 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 1701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 296 0.027 - 0.054: 87 0.054 - 0.081: 44 0.081 - 0.108: 20 0.108 - 0.135: 4 Chirality restraints: 451 Sorted by residual: chirality pdb=" CA VAL A 27 " pdb=" N VAL A 27 " pdb=" C VAL A 27 " pdb=" CB VAL A 27 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA ILE B 46 " pdb=" N ILE B 46 " pdb=" C ILE B 46 " pdb=" CB ILE B 46 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.41e-01 chirality pdb=" CA VAL B 73 " pdb=" N VAL B 73 " pdb=" C VAL B 73 " pdb=" CB VAL B 73 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.38e-01 ... (remaining 448 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 106 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO A 107 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 107 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 107 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 52 " -0.091 9.50e-02 1.11e+02 4.09e-02 1.28e+00 pdb=" NE ARG B 52 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG B 52 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 52 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 52 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 173 " 0.015 5.00e-02 4.00e+02 2.33e-02 8.66e-01 pdb=" N PRO A 174 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " 0.013 5.00e-02 4.00e+02 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 976 2.86 - 3.37: 2836 3.37 - 3.88: 4286 3.88 - 4.39: 4429 4.39 - 4.90: 8019 Nonbonded interactions: 20546 Sorted by model distance: nonbonded pdb=" NH2 ARG A 179 " pdb=" OXT GLY B 76 " model vdw 2.351 3.120 nonbonded pdb=" O GLY A 32 " pdb=" OG1 THR A 33 " model vdw 2.453 3.040 nonbonded pdb=" OE1 GLU A 277 " pdb=" OH TYR B 34 " model vdw 2.539 3.040 nonbonded pdb=" O GLY A 55 " pdb=" ND2 ASN A 59 " model vdw 2.540 3.120 nonbonded pdb=" O THR A 172 " pdb=" OG SER A 175 " model vdw 2.551 3.040 ... (remaining 20541 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.400 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 : 0.003 0.032 2899 Z= 0.136 Angle : 0.536 5.513 3951 Z= 0.292 Chirality : 0.037 0.135 451 Planarity : 0.003 0.041 488 Dihedral : 12.880 78.018 1022 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.75 (0.47), residues: 357 helix: 2.26 (0.32), residues: 265 sheet: -3.09 (1.68), residues: 10 loop : -2.11 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 52 TYR 0.006 0.001 TYR B 34 PHE 0.013 0.001 PHE A 143 TRP 0.008 0.001 TRP A 114 HIS 0.003 0.001 HIS B 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 ( 2895) covalent geometry : angle 0.53249 / 0.29 ( 3943) SS BOND : bond 0.00178 / 0.09 ( 4) SS BOND : angle 1.49107 / 0.82 ( 8) hydrogen bonds : bond 0.11113 / 8.45 ( 189) hydrogen bonds : angle 4.80909 / 3.67 ( 564) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 LEU cc_start: 0.8425 (tp) cc_final: 0.8009 (tp) REVERT: B 65 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7912 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.0657 time to fit residues: 7.5673 Evaluate side-chains 75 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.162180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.130507 restraints weight = 4283.354| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.06 r_work: 0.3507 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2899 Z= 0.159 Angle : 0.657 8.191 3951 Z= 0.320 Chirality : 0.042 0.173 451 Planarity : 0.004 0.031 488 Dihedral : 3.933 18.888 393 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.67 % Allowed : 14.38 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.92 (0.46), residues: 357 helix: 2.38 (0.32), residues: 266 sheet: -2.81 (1.73), residues: 10 loop : -2.13 (0.63), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 259 TYR 0.007 0.001 TYR B 34 PHE 0.006 0.001 PHE A 221 TRP 0.007 0.001 TRP A 238 HIS 0.017 0.002 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 2895) covalent geometry : angle 0.65449 / 0.32 ( 3943) SS BOND : bond 0.00185 / 0.09 ( 4) SS BOND : angle 1.53634 / 0.77 ( 8) hydrogen bonds : bond 0.04946 / 3.55 ( 189) hydrogen bonds : angle 4.11996 / 3.07 ( 564) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: A 103 LYS cc_start: 0.8004 (mmmt) cc_final: 0.7766 (tptm) REVERT: A 258 LEU cc_start: 0.8349 (tp) cc_final: 0.7816 (tp) REVERT: A 285 LEU cc_start: 0.8441 (tt) cc_final: 0.8211 (tp) REVERT: B 52 ARG cc_start: 0.8287 (tpt-90) cc_final: 0.7308 (tpp-160) outliers start: 5 outliers final: 4 residues processed: 72 average time/residue: 0.0495 time to fit residues: 4.3692 Evaluate side-chains 67 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 31 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.0570 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 0.0970 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 31 optimal weight: 0.0970 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.165654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.133892 restraints weight = 4278.628| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 3.06 r_work: 0.3535 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2899 Z= 0.128 Angle : 0.623 9.105 3951 Z= 0.303 Chirality : 0.039 0.146 451 Planarity : 0.004 0.029 488 Dihedral : 3.831 17.429 393 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.67 % Allowed : 18.39 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.02 (0.46), residues: 357 helix: 2.45 (0.32), residues: 266 sheet: -2.64 (1.72), residues: 10 loop : -2.13 (0.62), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 52 TYR 0.011 0.001 TYR A 299 PHE 0.005 0.001 PHE A 52 TRP 0.010 0.001 TRP A 114 HIS 0.008 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 ( 2895) covalent geometry : angle 0.62041 / 0.30 ( 3943) SS BOND : bond 0.00308 / 0.15 ( 4) SS BOND : angle 1.45153 / 0.69 ( 8) hydrogen bonds : bond 0.04396 / 3.12 ( 189) hydrogen bonds : angle 3.83941 / 2.81 ( 564) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.063 Fit side-chains revert: symmetry clash REVERT: A 103 LYS cc_start: 0.7847 (mmmt) cc_final: 0.7618 (tptm) REVERT: A 258 LEU cc_start: 0.8254 (tp) cc_final: 0.7738 (tp) REVERT: A 302 ARG cc_start: 0.7657 (mtm-85) cc_final: 0.7397 (mtp-110) REVERT: B 26 TYR cc_start: 0.9155 (m-80) cc_final: 0.8873 (m-80) outliers start: 2 outliers final: 2 residues processed: 70 average time/residue: 0.0443 time to fit residues: 3.7125 Evaluate side-chains 66 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 31 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.0370 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.162042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.130471 restraints weight = 4215.233| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.06 r_work: 0.3522 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2899 Z= 0.143 Angle : 0.640 10.108 3951 Z= 0.317 Chirality : 0.041 0.245 451 Planarity : 0.004 0.033 488 Dihedral : 3.987 22.677 393 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.01 % Allowed : 16.72 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.92 (0.46), residues: 357 helix: 2.36 (0.32), residues: 265 sheet: -2.57 (1.70), residues: 10 loop : -2.03 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 52 TYR 0.010 0.001 TYR A 48 PHE 0.006 0.001 PHE A 52 TRP 0.008 0.001 TRP A 114 HIS 0.007 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 2895) covalent geometry : angle 0.63226 / 0.31 ( 3943) SS BOND : bond 0.01054 / 0.50 ( 4) SS BOND : angle 2.34109 / 1.32 ( 8) hydrogen bonds : bond 0.04507 / 3.24 ( 189) hydrogen bonds : angle 3.94215 / 2.84 ( 564) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 LEU cc_start: 0.8245 (tp) cc_final: 0.7712 (tp) REVERT: A 302 ARG cc_start: 0.7615 (mtm-85) cc_final: 0.7313 (mtp-110) outliers start: 6 outliers final: 2 residues processed: 70 average time/residue: 0.0473 time to fit residues: 3.9134 Evaluate side-chains 62 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 0.0170 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 237 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.162510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.131174 restraints weight = 4233.373| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 3.05 r_work: 0.3508 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2899 Z= 0.149 Angle : 0.671 9.123 3951 Z= 0.330 Chirality : 0.040 0.196 451 Planarity : 0.004 0.035 488 Dihedral : 4.020 20.074 393 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.67 % Allowed : 18.06 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.46), residues: 357 helix: 2.41 (0.32), residues: 264 sheet: -2.49 (1.70), residues: 10 loop : -2.01 (0.63), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 210 TYR 0.010 0.001 TYR A 299 PHE 0.006 0.001 PHE A 52 TRP 0.008 0.001 TRP A 114 HIS 0.007 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 2895) covalent geometry : angle 0.66683 / 0.33 ( 3943) SS BOND : bond 0.00448 / 0.21 ( 4) SS BOND : angle 1.86150 / 1.00 ( 8) hydrogen bonds : bond 0.04648 / 3.35 ( 189) hydrogen bonds : angle 3.89311 / 2.82 ( 564) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.2410 (ptt) cc_final: 0.1978 (ptt) REVERT: A 258 LEU cc_start: 0.8267 (tp) cc_final: 0.7802 (tp) REVERT: A 302 ARG cc_start: 0.7687 (mtm-85) cc_final: 0.7401 (mtp-110) REVERT: B 56 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7816 (mp0) outliers start: 5 outliers final: 5 residues processed: 65 average time/residue: 0.0566 time to fit residues: 4.4133 Evaluate side-chains 66 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.161831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.130720 restraints weight = 4211.254| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 3.02 r_work: 0.3517 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2899 Z= 0.137 Angle : 0.628 8.959 3951 Z= 0.313 Chirality : 0.039 0.164 451 Planarity : 0.004 0.038 488 Dihedral : 3.978 19.632 393 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.01 % Allowed : 17.73 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.46), residues: 357 helix: 2.46 (0.32), residues: 265 sheet: -2.44 (1.70), residues: 10 loop : -2.09 (0.62), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 210 TYR 0.010 0.001 TYR A 48 PHE 0.006 0.001 PHE A 52 TRP 0.009 0.001 TRP A 114 HIS 0.005 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 2895) covalent geometry : angle 0.62408 / 0.31 ( 3943) SS BOND : bond 0.00459 / 0.22 ( 4) SS BOND : angle 1.64499 / 0.89 ( 8) hydrogen bonds : bond 0.04467 / 3.21 ( 189) hydrogen bonds : angle 3.80338 / 2.74 ( 564) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.2395 (ptt) cc_final: 0.2044 (ptt) REVERT: A 258 LEU cc_start: 0.8248 (tp) cc_final: 0.7787 (tp) REVERT: A 302 ARG cc_start: 0.7553 (mtm-85) cc_final: 0.7280 (mtp-110) REVERT: B 12 GLN cc_start: 0.8547 (tp-100) cc_final: 0.8165 (tp-100) outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.0490 time to fit residues: 4.0716 Evaluate side-chains 67 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.0670 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.160606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.129003 restraints weight = 4280.913| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.05 r_work: 0.3490 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2899 Z= 0.161 Angle : 0.678 9.652 3951 Z= 0.330 Chirality : 0.040 0.152 451 Planarity : 0.004 0.038 488 Dihedral : 4.022 18.181 393 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.01 % Allowed : 19.06 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.90 (0.46), residues: 357 helix: 2.37 (0.32), residues: 265 sheet: -2.50 (1.69), residues: 10 loop : -2.16 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 231 TYR 0.009 0.001 TYR A 48 PHE 0.007 0.001 PHE A 52 TRP 0.007 0.001 TRP A 78 HIS 0.006 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 2895) covalent geometry : angle 0.67474 / 0.33 ( 3943) SS BOND : bond 0.00490 / 0.23 ( 4) SS BOND : angle 1.64786 / 0.89 ( 8) hydrogen bonds : bond 0.04786 / 3.43 ( 189) hydrogen bonds : angle 3.86578 / 2.80 ( 564) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.061 Fit side-chains revert: symmetry clash REVERT: A 184 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7720 (tt0) REVERT: A 233 MET cc_start: 0.2894 (ptt) cc_final: 0.2594 (ptt) REVERT: A 258 LEU cc_start: 0.8281 (tp) cc_final: 0.7810 (tp) REVERT: A 302 ARG cc_start: 0.7542 (mtm-85) cc_final: 0.7267 (mtp-110) REVERT: B 12 GLN cc_start: 0.8584 (tp-100) cc_final: 0.8179 (tp-100) REVERT: B 52 ARG cc_start: 0.8825 (tpt170) cc_final: 0.8381 (tpt-90) REVERT: B 56 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7557 (mt-10) outliers start: 6 outliers final: 6 residues processed: 71 average time/residue: 0.0475 time to fit residues: 4.0223 Evaluate side-chains 71 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.0060 chunk 3 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 HIS ** 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 = 0.3989 r_free = 0.3989 target = 0.162090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.130496 restraints weight = 4316.542| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 3.08 r_work: 0.3501 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2899 Z= 0.142 Angle : 0.637 8.198 3951 Z= 0.319 Chirality : 0.039 0.143 451 Planarity : 0.004 0.042 488 Dihedral : 4.051 17.408 393 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.34 % Allowed : 19.73 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.90 (0.46), residues: 357 helix: 2.39 (0.32), residues: 265 sheet: -2.44 (1.69), residues: 10 loop : -2.23 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 210 TYR 0.009 0.001 TYR A 48 PHE 0.006 0.001 PHE A 52 TRP 0.009 0.001 TRP A 114 HIS 0.006 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 2895) covalent geometry : angle 0.63461 / 0.32 ( 3943) SS BOND : bond 0.00481 / 0.23 ( 4) SS BOND : angle 1.43524 / 0.78 ( 8) hydrogen bonds : bond 0.04579 / 3.29 ( 189) hydrogen bonds : angle 3.76207 / 2.70 ( 564) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7683 (tt0) REVERT: A 233 MET cc_start: 0.2962 (ptt) cc_final: 0.2660 (ptt) REVERT: A 302 ARG cc_start: 0.7487 (mtm-85) cc_final: 0.7216 (mtp-110) REVERT: B 12 GLN cc_start: 0.8553 (tp-100) cc_final: 0.8175 (tp-100) REVERT: B 52 ARG cc_start: 0.8827 (tpt170) cc_final: 0.8456 (tpt-90) outliers start: 7 outliers final: 6 residues processed: 73 average time/residue: 0.0485 time to fit residues: 4.1605 Evaluate side-chains 70 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 3 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.160729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.129336 restraints weight = 4329.668| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.09 r_work: 0.3488 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2899 Z= 0.158 Angle : 0.681 10.148 3951 Z= 0.332 Chirality : 0.040 0.137 451 Planarity : 0.004 0.040 488 Dihedral : 4.013 17.840 393 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.67 % Allowed : 19.73 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.86 (0.46), residues: 357 helix: 2.36 (0.32), residues: 265 sheet: -2.46 (1.68), residues: 10 loop : -2.25 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 274 TYR 0.009 0.001 TYR A 48 PHE 0.007 0.001 PHE A 52 TRP 0.008 0.001 TRP A 114 HIS 0.016 0.002 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 2895) covalent geometry : angle 0.67743 / 0.33 ( 3943) SS BOND : bond 0.00439 / 0.21 ( 4) SS BOND : angle 1.64826 / 0.89 ( 8) hydrogen bonds : bond 0.04737 / 3.40 ( 189) hydrogen bonds : angle 3.85783 / 2.77 ( 564) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: A 184 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7668 (tt0) REVERT: A 233 MET cc_start: 0.3170 (ptt) cc_final: 0.2820 (ptt) REVERT: A 258 LEU cc_start: 0.8266 (tp) cc_final: 0.7802 (tp) REVERT: A 302 ARG cc_start: 0.7551 (mtm-85) cc_final: 0.7249 (mtp-110) REVERT: B 12 GLN cc_start: 0.8583 (tp-100) cc_final: 0.8175 (tp-100) REVERT: B 52 ARG cc_start: 0.8848 (tpt170) cc_final: 0.8449 (tpt-90) outliers start: 5 outliers final: 5 residues processed: 69 average time/residue: 0.0724 time to fit residues: 5.9032 Evaluate side-chains 70 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.159854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.128774 restraints weight = 4236.596| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 3.01 r_work: 0.3495 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2899 Z= 0.161 Angle : 0.670 8.390 3951 Z= 0.336 Chirality : 0.042 0.198 451 Planarity : 0.004 0.044 488 Dihedral : 4.149 21.371 393 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.67 % Allowed : 20.07 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.81 (0.46), residues: 357 helix: 2.28 (0.32), residues: 266 sheet: -2.45 (1.68), residues: 10 loop : -2.17 (0.63), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 274 TYR 0.010 0.001 TYR A 299 PHE 0.007 0.001 PHE A 52 TRP 0.008 0.001 TRP A 114 HIS 0.005 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 2895) covalent geometry : angle 0.66716 / 0.33 ( 3943) SS BOND : bond 0.00496 / 0.24 ( 4) SS BOND : angle 1.54639 / 0.82 ( 8) hydrogen bonds : bond 0.04793 / 3.44 ( 189) hydrogen bonds : angle 3.87130 / 2.77 ( 564) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: A 184 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7657 (tt0) REVERT: A 233 MET cc_start: 0.3373 (ptt) cc_final: 0.3045 (ptt) REVERT: A 302 ARG cc_start: 0.7561 (mtm-85) cc_final: 0.7259 (mtp-110) REVERT: B 12 GLN cc_start: 0.8599 (tp-100) cc_final: 0.8182 (tp-100) REVERT: B 56 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7799 (mp0) outliers start: 5 outliers final: 5 residues processed: 65 average time/residue: 0.0795 time to fit residues: 6.0651 Evaluate side-chains 68 residues out of total 299 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 34 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.162399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.130795 restraints weight = 4223.147| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.10 r_work: 0.3511 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2899 Z= 0.137 Angle : 0.660 9.188 3951 Z= 0.328 Chirality : 0.040 0.176 451 Planarity : 0.004 0.044 488 Dihedral : 4.052 21.447 393 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.00 % Allowed : 21.40 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.90 (0.46), residues: 357 helix: 2.38 (0.32), residues: 265 sheet: -2.37 (1.69), residues: 10 loop : -2.20 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 274 TYR 0.011 0.001 TYR A 299 PHE 0.014 0.001 PHE B 54 TRP 0.011 0.001 TRP A 114 HIS 0.003 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 2895) covalent geometry : angle 0.65701 / 0.33 ( 3943) SS BOND : bond 0.00386 / 0.19 ( 4) SS BOND : angle 1.50738 / 0.80 ( 8) hydrogen bonds : bond 0.04434 / 3.17 ( 189) hydrogen bonds : angle 3.80420 / 2.69 ( 564) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 765.48 seconds wall clock time: 13 minutes 45.26 seconds (825.26 seconds total)