Starting phenix.real_space_refine on Wed Jun 3 11:58:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o7g_70198/06_2026/9o7g_70198.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o7g_70198/06_2026/9o7g_70198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o7g_70198/06_2026/9o7g_70198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o7g_70198/06_2026/9o7g_70198.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o7g_70198/06_2026/9o7g_70198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o7g_70198/06_2026/9o7g_70198.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 12 5.16 5 C 1447 2.51 5 N 392 2.21 5 O 459 1.98 5 H 2234 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4544 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1812 Classifications: {'peptide': 121} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "B" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1149 Classifications: {'peptide': 72} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 65} Chain: "D" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1583 Classifications: {'peptide': 110} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Time building chain proxies: 1.22, per 1000 atoms: 0.27 Number of scatterers: 4544 At special positions: 0 Unit cell: (62.55, 60.048, 75.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 O 459 8.00 N 392 7.00 C 1447 6.00 H 2234 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 100 " distance=2.02 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 104 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 113.5 milliseconds 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 544 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 6 sheets defined 13.9% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 283 through 295 Processing helix chain 'D' and resid 95 through 99 Processing sheet with id=AA1, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.759A pdb=" N GLY C 37 " --> pdb=" O SER C 103 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE C 38 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TRP C 54 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP C 40 " --> pdb=" O MET C 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 22 through 27 Processing sheet with id=AA3, first strand: chain 'B' and resid 251 through 253 removed outlier: 3.705A pdb=" N ILE B 281 " --> pdb=" O ILE B 245 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 24 through 27 removed outlier: 5.840A pdb=" N GLN D 53 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU D 62 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 24 through 27 Processing sheet with id=AA6, first strand: chain 'D' and resid 33 through 38 87 hydrogen bonds defined for protein. 210 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: 0.98 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 2232 1.13 - 1.30: 407 1.30 - 1.48: 918 1.48 - 1.65: 1019 1.65 - 1.82: 18 Bond restraints: 4594 Sorted by residual: bond pdb=" N THR D 85 " pdb=" H THR D 85 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N VAL C 72 " pdb=" H VAL C 72 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLN B 262 " pdb=" H GLN B 262 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" NE2 GLN C 43 " pdb="HE21 GLN C 43 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LEU B 280 " pdb=" H LEU B 280 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 4589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 6726 2.34 - 4.67: 1190 4.67 - 7.01: 298 7.01 - 9.35: 40 9.35 - 11.69: 4 Bond angle restraints: 8258 Sorted by residual: angle pdb=" CA ASP B 253 " pdb=" CB ASP B 253 " pdb=" CG ASP B 253 " ideal model delta sigma weight residual 112.60 108.05 4.55 1.00e+00 1.00e+00 2.07e+01 angle pdb=" CB HIS B 266 " pdb=" CG HIS B 266 " pdb=" CD2 HIS B 266 " ideal model delta sigma weight residual 131.20 125.72 5.48 1.30e+00 5.92e-01 1.78e+01 angle pdb=" CB HIS B 260 " pdb=" CG HIS B 260 " pdb=" CD2 HIS B 260 " ideal model delta sigma weight residual 131.20 125.76 5.44 1.30e+00 5.92e-01 1.75e+01 angle pdb=" OE1 GLN B 262 " pdb=" CD GLN B 262 " pdb=" NE2 GLN B 262 " ideal model delta sigma weight residual 122.60 118.51 4.09 1.00e+00 1.00e+00 1.67e+01 angle pdb=" OE1 GLN D 53 " pdb=" CD GLN D 53 " pdb=" NE2 GLN D 53 " ideal model delta sigma weight residual 122.60 118.51 4.09 1.00e+00 1.00e+00 1.67e+01 ... (remaining 8253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 2017 16.55 - 33.09: 106 33.09 - 49.64: 51 49.64 - 66.19: 19 66.19 - 82.73: 3 Dihedral angle restraints: 2196 sinusoidal: 1190 harmonic: 1006 Sorted by residual: dihedral pdb=" CA SER C 29 " pdb=" C SER C 29 " pdb=" N GLY C 30 " pdb=" CA GLY C 30 " ideal model delta harmonic sigma weight residual 180.00 150.81 29.19 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA GLY C 30 " pdb=" C GLY C 30 " pdb=" N TYR C 31 " pdb=" CA TYR C 31 " ideal model delta harmonic sigma weight residual 180.00 -151.17 -28.83 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA THR C 32 " pdb=" C THR C 32 " pdb=" N PHE C 33 " pdb=" CA PHE C 33 " ideal model delta harmonic sigma weight residual -180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 2193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 180 0.068 - 0.136: 124 0.136 - 0.203: 43 0.203 - 0.271: 6 0.271 - 0.339: 2 Chirality restraints: 355 Sorted by residual: chirality pdb=" CA GLN C 10 " pdb=" N GLN C 10 " pdb=" C GLN C 10 " pdb=" CB GLN C 10 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA ASN D 43 " pdb=" N ASN D 43 " pdb=" C ASN D 43 " pdb=" CB ASN D 43 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA CYS D 37 " pdb=" N CYS D 37 " pdb=" C CYS D 37 " pdb=" CB CYS D 37 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 352 not shown) Planarity restraints: 700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 115 " -0.154 2.00e-02 2.50e+03 7.47e-02 1.67e+02 pdb=" CG PHE C 115 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE C 115 " 0.092 2.00e-02 2.50e+03 pdb=" CD2 PHE C 115 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE C 115 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 115 " 0.044 2.00e-02 2.50e+03 pdb=" CZ PHE C 115 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE C 115 " 0.104 2.00e-02 2.50e+03 pdb=" HD2 PHE C 115 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 PHE C 115 " -0.114 2.00e-02 2.50e+03 pdb=" HE2 PHE C 115 " 0.030 2.00e-02 2.50e+03 pdb=" HZ PHE C 115 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 31 " -0.143 2.00e-02 2.50e+03 5.66e-02 9.61e+01 pdb=" CG TYR C 31 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR C 31 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR C 31 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR C 31 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR C 31 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR C 31 " -0.030 2.00e-02 2.50e+03 pdb=" OH TYR C 31 " -0.079 2.00e-02 2.50e+03 pdb=" HD1 TYR C 31 " 0.041 2.00e-02 2.50e+03 pdb=" HD2 TYR C 31 " 0.065 2.00e-02 2.50e+03 pdb=" HE1 TYR C 31 " 0.026 2.00e-02 2.50e+03 pdb=" HE2 TYR C 31 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 54 " -0.056 2.00e-02 2.50e+03 3.98e-02 6.33e+01 pdb=" CG TRP C 54 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TRP C 54 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP C 54 " -0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP C 54 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 54 " -0.037 2.00e-02 2.50e+03 pdb=" CE3 TRP C 54 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 54 " -0.046 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 54 " 0.017 2.00e-02 2.50e+03 pdb=" CH2 TRP C 54 " -0.011 2.00e-02 2.50e+03 pdb=" HD1 TRP C 54 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP C 54 " 0.112 2.00e-02 2.50e+03 pdb=" HE3 TRP C 54 " 0.032 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 54 " -0.051 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 54 " 0.043 2.00e-02 2.50e+03 pdb=" HH2 TRP C 54 " -0.000 2.00e-02 2.50e+03 ... (remaining 697 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 387 2.21 - 2.81: 8100 2.81 - 3.41: 12323 3.41 - 4.00: 16593 4.00 - 4.60: 23922 Nonbonded interactions: 61325 Sorted by model distance: nonbonded pdb=" OD2 ASP C 77 " pdb=" HG1 THR C 80 " model vdw 1.614 2.450 nonbonded pdb=" OD1 ASP C 77 " pdb=" HG SER C 79 " model vdw 1.641 2.450 nonbonded pdb=" HH TYR B 252 " pdb=" OD1 ASP B 268 " model vdw 1.647 2.450 nonbonded pdb=" HG1 THR B 246 " pdb=" OD2 ASP B 268 " model vdw 1.655 2.450 nonbonded pdb=" HG1 THR B 276 " pdb=" O GLU B 278 " model vdw 1.680 2.450 ... (remaining 61320 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: 3.130 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: 0.040 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.780 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 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 0.038 2362 Z= 0.827 Angle : 1.770 7.984 3211 Z= 1.178 Chirality : 0.095 0.339 355 Planarity : 0.012 0.092 415 Dihedral : 12.545 82.730 846 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 1.35 % Allowed : 5.39 % Favored : 93.27 % Rotamer: Outliers : 0.40 % Allowed : 0.79 % Favored : 98.81 % 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: -0.38 (0.48), residues: 297 helix: -1.09 (0.89), residues: 25 sheet: 0.29 (0.55), residues: 95 loop : -0.38 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 263 TYR 0.114 0.019 TYR C 31 PHE 0.097 0.012 PHE C 115 TRP 0.058 0.017 TRP C 118 HIS 0.003 0.002 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.01381 / 0.83 ( 2360) covalent geometry : angle 1.77026 / 1.18 ( 3207) SS BOND : bond 0.01274 / 0.65 ( 2) SS BOND : angle 1.65784 / 0.81 ( 4) hydrogen bonds : bond 0.15520 / 10.07 ( 80) hydrogen bonds : angle 7.74558 / 5.24 ( 210) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 32 THR cc_start: 0.7590 (m) cc_final: 0.7315 (t) REVERT: B 237 PHE cc_start: 0.7824 (m-80) cc_final: 0.7557 (m-10) REVERT: D 122 ARG cc_start: 0.7253 (tpp80) cc_final: 0.7011 (tpp80) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.2051 time to fit residues: 25.0543 Evaluate side-chains 72 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.138007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.127756 restraints weight = 17459.519| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 3.29 r_work: 0.3970 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2362 Z= 0.160 Angle : 0.679 7.358 3211 Z= 0.370 Chirality : 0.045 0.140 355 Planarity : 0.005 0.038 415 Dihedral : 6.051 32.674 328 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.39 % Favored : 94.28 % Rotamer: Outliers : 1.19 % Allowed : 12.25 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.48), residues: 297 helix: 1.93 (1.19), residues: 25 sheet: -0.09 (0.48), residues: 100 loop : -0.33 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 122 TYR 0.013 0.002 TYR C 31 PHE 0.008 0.002 PHE C 115 TRP 0.006 0.001 TRP C 118 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 2360) covalent geometry : angle 0.67859 / 0.37 ( 3207) SS BOND : bond 0.00865 / 0.43 ( 2) SS BOND : angle 0.71278 / 0.36 ( 4) hydrogen bonds : bond 0.04326 / 2.76 ( 80) hydrogen bonds : angle 6.33478 / 4.27 ( 210) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 17 LYS cc_start: 0.1526 (mmtt) cc_final: 0.1216 (mmtt) REVERT: B 259 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7627 (tp30) REVERT: B 288 GLU cc_start: 0.6141 (tm-30) cc_final: 0.5856 (tm-30) outliers start: 3 outliers final: 3 residues processed: 74 average time/residue: 0.1509 time to fit residues: 12.8594 Evaluate side-chains 59 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 281 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.137232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.127556 restraints weight = 17788.234| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 3.21 r_work: 0.3975 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2362 Z= 0.120 Angle : 0.597 6.534 3211 Z= 0.320 Chirality : 0.043 0.130 355 Planarity : 0.005 0.047 415 Dihedral : 5.459 28.783 328 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.38 % Favored : 95.29 % Rotamer: Outliers : 1.58 % Allowed : 15.42 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.50), residues: 297 helix: 2.15 (1.19), residues: 25 sheet: -0.29 (0.49), residues: 101 loop : -0.08 (0.50), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 122 TYR 0.017 0.001 TYR C 31 PHE 0.006 0.001 PHE C 99 TRP 0.005 0.001 TRP C 118 HIS 0.001 0.000 HIS B 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 2360) covalent geometry : angle 0.59678 / 0.32 ( 3207) SS BOND : bond 0.00498 / 0.24 ( 2) SS BOND : angle 0.73966 / 0.37 ( 4) hydrogen bonds : bond 0.03499 / 2.22 ( 80) hydrogen bonds : angle 5.51760 / 3.73 ( 210) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 10 GLN cc_start: 0.6567 (mt0) cc_final: 0.6302 (mt0) REVERT: C 17 LYS cc_start: 0.1417 (mmtt) cc_final: 0.0893 (mmtt) REVERT: B 259 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7540 (tp30) REVERT: B 281 ILE cc_start: 0.6602 (mt) cc_final: 0.5923 (pt) REVERT: B 288 GLU cc_start: 0.6170 (tm-30) cc_final: 0.5916 (tm-30) outliers start: 4 outliers final: 4 residues processed: 64 average time/residue: 0.1819 time to fit residues: 13.2169 Evaluate side-chains 61 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.0040 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.0070 chunk 26 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.3410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.137749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.128166 restraints weight = 17703.947| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 3.27 r_work: 0.3977 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2362 Z= 0.100 Angle : 0.550 5.881 3211 Z= 0.292 Chirality : 0.043 0.136 355 Planarity : 0.005 0.048 415 Dihedral : 5.168 27.393 328 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.79 % Allowed : 16.60 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.51), residues: 297 helix: 1.93 (1.13), residues: 25 sheet: -0.31 (0.51), residues: 101 loop : 0.09 (0.52), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 122 TYR 0.015 0.001 TYR C 31 PHE 0.004 0.001 PHE C 99 TRP 0.005 0.001 TRP C 54 HIS 0.001 0.000 HIS B 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 2360) covalent geometry : angle 0.54942 / 0.29 ( 3207) SS BOND : bond 0.00439 / 0.21 ( 2) SS BOND : angle 0.64129 / 0.33 ( 4) hydrogen bonds : bond 0.03040 / 1.97 ( 80) hydrogen bonds : angle 5.15273 / 3.46 ( 210) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 281 ILE cc_start: 0.6611 (mt) cc_final: 0.5953 (pt) REVERT: B 288 GLU cc_start: 0.6103 (tm-30) cc_final: 0.5903 (tm-30) outliers start: 2 outliers final: 2 residues processed: 65 average time/residue: 0.1830 time to fit residues: 13.3440 Evaluate side-chains 59 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain B residue 276 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.0980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.134571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.125415 restraints weight = 17505.045| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 3.13 r_work: 0.3956 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2362 Z= 0.135 Angle : 0.573 6.300 3211 Z= 0.303 Chirality : 0.042 0.138 355 Planarity : 0.005 0.048 415 Dihedral : 5.100 28.001 328 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.37 % Allowed : 14.23 % Favored : 83.40 % 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: 0.17 (0.52), residues: 297 helix: 2.06 (1.14), residues: 25 sheet: -0.15 (0.52), residues: 99 loop : 0.09 (0.53), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 122 TYR 0.012 0.001 TYR C 31 PHE 0.006 0.001 PHE C 99 TRP 0.007 0.001 TRP C 118 HIS 0.001 0.000 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 2360) covalent geometry : angle 0.57305 / 0.30 ( 3207) SS BOND : bond 0.00498 / 0.24 ( 2) SS BOND : angle 0.80296 / 0.41 ( 4) hydrogen bonds : bond 0.03116 / 1.99 ( 80) hydrogen bonds : angle 5.09416 / 3.39 ( 210) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 281 ILE cc_start: 0.6636 (mt) cc_final: 0.5988 (pt) REVERT: B 288 GLU cc_start: 0.5967 (tm-30) cc_final: 0.5763 (tm-30) outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 0.1344 time to fit residues: 9.5783 Evaluate side-chains 59 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 0.0970 chunk 8 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.134530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.125328 restraints weight = 17508.652| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 3.13 r_work: 0.3965 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2362 Z= 0.116 Angle : 0.561 5.785 3211 Z= 0.294 Chirality : 0.043 0.134 355 Planarity : 0.005 0.048 415 Dihedral : 5.072 27.484 328 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.58 % Allowed : 15.81 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.53), residues: 297 helix: 1.99 (1.13), residues: 25 sheet: -0.16 (0.53), residues: 99 loop : 0.09 (0.53), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 122 TYR 0.013 0.001 TYR C 31 PHE 0.004 0.001 PHE B 237 TRP 0.007 0.001 TRP D 107 HIS 0.001 0.000 HIS B 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 2360) covalent geometry : angle 0.56036 / 0.29 ( 3207) SS BOND : bond 0.00399 / 0.19 ( 2) SS BOND : angle 0.74919 / 0.38 ( 4) hydrogen bonds : bond 0.02979 / 1.91 ( 80) hydrogen bonds : angle 4.97976 / 3.30 ( 210) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 TRP cc_start: 0.7629 (t60) cc_final: 0.7019 (t60) REVERT: B 281 ILE cc_start: 0.6561 (mt) cc_final: 0.5938 (pt) outliers start: 4 outliers final: 2 residues processed: 58 average time/residue: 0.1125 time to fit residues: 7.9250 Evaluate side-chains 54 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 0.0670 chunk 26 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.134356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.125114 restraints weight = 17600.148| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 3.12 r_work: 0.3958 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.6404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2362 Z= 0.119 Angle : 0.559 5.881 3211 Z= 0.293 Chirality : 0.042 0.131 355 Planarity : 0.005 0.049 415 Dihedral : 4.992 26.441 328 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.77 % Allowed : 13.44 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.53), residues: 297 helix: 1.97 (1.12), residues: 25 sheet: -0.21 (0.52), residues: 99 loop : 0.09 (0.54), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 122 TYR 0.014 0.001 TYR C 31 PHE 0.005 0.001 PHE B 237 TRP 0.007 0.001 TRP D 107 HIS 0.001 0.000 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 2360) covalent geometry : angle 0.55872 / 0.29 ( 3207) SS BOND : bond 0.00403 / 0.19 ( 2) SS BOND : angle 0.74258 / 0.38 ( 4) hydrogen bonds : bond 0.02903 / 1.85 ( 80) hydrogen bonds : angle 4.90973 / 3.25 ( 210) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 7 GLN cc_start: 0.8056 (pt0) cc_final: 0.7784 (pp30) REVERT: C 54 TRP cc_start: 0.7652 (t60) cc_final: 0.7057 (t60) REVERT: B 281 ILE cc_start: 0.6573 (mt) cc_final: 0.5985 (pt) outliers start: 7 outliers final: 5 residues processed: 56 average time/residue: 0.1073 time to fit residues: 7.3254 Evaluate side-chains 57 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.134303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.124916 restraints weight = 17587.804| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 3.17 r_work: 0.3956 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.6493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2362 Z= 0.119 Angle : 0.559 5.930 3211 Z= 0.291 Chirality : 0.042 0.132 355 Planarity : 0.005 0.050 415 Dihedral : 5.022 26.494 328 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.98 % Allowed : 15.02 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.53), residues: 297 helix: 1.55 (1.11), residues: 25 sheet: -0.19 (0.52), residues: 105 loop : 0.11 (0.56), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 122 TYR 0.013 0.001 TYR C 31 PHE 0.005 0.001 PHE B 237 TRP 0.006 0.001 TRP D 107 HIS 0.001 0.000 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 2360) covalent geometry : angle 0.55832 / 0.29 ( 3207) SS BOND : bond 0.00385 / 0.18 ( 2) SS BOND : angle 0.69911 / 0.35 ( 4) hydrogen bonds : bond 0.02933 / 1.89 ( 80) hydrogen bonds : angle 4.93713 / 3.28 ( 210) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 7 GLN cc_start: 0.8088 (pt0) cc_final: 0.7825 (pp30) REVERT: C 54 TRP cc_start: 0.7675 (t60) cc_final: 0.7085 (t60) REVERT: B 259 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7625 (mm-30) REVERT: B 281 ILE cc_start: 0.6529 (mt) cc_final: 0.5954 (pt) outliers start: 5 outliers final: 4 residues processed: 57 average time/residue: 0.1017 time to fit residues: 7.1130 Evaluate side-chains 55 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.132716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.123463 restraints weight = 17713.092| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 3.06 r_work: 0.3938 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.6645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2362 Z= 0.136 Angle : 0.578 5.997 3211 Z= 0.301 Chirality : 0.042 0.135 355 Planarity : 0.005 0.049 415 Dihedral : 5.038 26.407 328 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.98 % Allowed : 15.02 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.53), residues: 297 helix: 1.53 (1.11), residues: 25 sheet: -0.26 (0.52), residues: 105 loop : 0.05 (0.55), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 122 TYR 0.013 0.001 TYR C 31 PHE 0.005 0.001 PHE D 117 TRP 0.007 0.001 TRP C 118 HIS 0.001 0.000 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 2360) covalent geometry : angle 0.57796 / 0.30 ( 3207) SS BOND : bond 0.00398 / 0.19 ( 2) SS BOND : angle 0.69845 / 0.35 ( 4) hydrogen bonds : bond 0.02998 / 1.93 ( 80) hydrogen bonds : angle 4.98554 / 3.32 ( 210) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 7 GLN cc_start: 0.8065 (pt0) cc_final: 0.7831 (pp30) REVERT: C 54 TRP cc_start: 0.7695 (t60) cc_final: 0.7131 (t60) REVERT: B 281 ILE cc_start: 0.6553 (mt) cc_final: 0.5974 (pt) outliers start: 5 outliers final: 5 residues processed: 55 average time/residue: 0.1012 time to fit residues: 6.8685 Evaluate side-chains 56 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 0.0370 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.133436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.124224 restraints weight = 17688.797| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 3.06 r_work: 0.3949 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.6773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2362 Z= 0.112 Angle : 0.558 5.777 3211 Z= 0.289 Chirality : 0.042 0.136 355 Planarity : 0.005 0.050 415 Dihedral : 4.951 25.520 328 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.37 % Allowed : 14.23 % Favored : 83.40 % 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: -0.01 (0.53), residues: 297 helix: 1.57 (1.10), residues: 25 sheet: -0.29 (0.52), residues: 105 loop : 0.07 (0.55), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 263 TYR 0.014 0.001 TYR C 31 PHE 0.006 0.001 PHE C 99 TRP 0.005 0.001 TRP C 118 HIS 0.001 0.000 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 2360) covalent geometry : angle 0.55806 / 0.29 ( 3207) SS BOND : bond 0.00376 / 0.18 ( 2) SS BOND : angle 0.67066 / 0.34 ( 4) hydrogen bonds : bond 0.02894 / 1.87 ( 80) hydrogen bonds : angle 4.86265 / 3.24 ( 210) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 10 GLN cc_start: 0.6935 (mt0) cc_final: 0.6146 (mt0) REVERT: C 54 TRP cc_start: 0.7687 (t60) cc_final: 0.7120 (t60) REVERT: B 281 ILE cc_start: 0.6561 (mt) cc_final: 0.5999 (pt) outliers start: 6 outliers final: 5 residues processed: 56 average time/residue: 0.0938 time to fit residues: 6.5488 Evaluate side-chains 55 residues out of total 253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain D residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.132403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.123084 restraints weight = 17899.554| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 3.08 r_work: 0.3917 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.6904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2362 Z= 0.122 Angle : 0.570 5.879 3211 Z= 0.297 Chirality : 0.042 0.137 355 Planarity : 0.005 0.050 415 Dihedral : 4.969 24.847 328 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.58 % Allowed : 14.62 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.54), residues: 297 helix: 1.59 (1.09), residues: 25 sheet: -0.25 (0.53), residues: 105 loop : 0.07 (0.56), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 263 TYR 0.014 0.001 TYR C 31 PHE 0.005 0.001 PHE B 237 TRP 0.006 0.001 TRP C 118 HIS 0.001 0.000 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 2360) covalent geometry : angle 0.57008 / 0.30 ( 3207) SS BOND : bond 0.00384 / 0.18 ( 2) SS BOND : angle 0.64036 / 0.32 ( 4) hydrogen bonds : bond 0.02859 / 1.84 ( 80) hydrogen bonds : angle 4.87876 / 3.25 ( 210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1870.99 seconds wall clock time: 32 minutes 32.27 seconds (1952.27 seconds total)