Starting phenix.real_space_refine on Fri Aug 22 12:54:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g8e_29846/08_2025/8g8e_29846.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8e_29846/08_2025/8g8e_29846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g8e_29846/08_2025/8g8e_29846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8e_29846/08_2025/8g8e_29846.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g8e_29846/08_2025/8g8e_29846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8e_29846/08_2025/8g8e_29846.map" } resolution = 4.2 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= 0.002 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 P 64 5.49 5 S 5 5.16 5 C 1357 2.51 5 N 453 2.21 5 O 585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2464 Number of models: 1 Model: "" Number of chains: 3 Chain: "J" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 661 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "I" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 651 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "X" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1152 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Time building chain proxies: 0.78, per 1000 atoms: 0.32 Number of scatterers: 2464 At special positions: 0 Unit cell: (69.96, 76.32, 115.54, 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 5 16.00 P 64 15.00 O 585 8.00 N 453 7.00 C 1357 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 66.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 266 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 0 sheets defined 81.4% alpha, 0.0% beta 31 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'X' and resid 141 through 161 Processing helix chain 'X' and resid 163 through 176 Processing helix chain 'X' and resid 180 through 189 removed outlier: 3.554A pdb=" N ILE X 184 " --> pdb=" O SER X 180 " (cutoff:3.500A) Processing helix chain 'X' and resid 193 through 211 Proline residue: X 202 - end of helix Processing helix chain 'X' and resid 215 through 220 Processing helix chain 'X' and resid 238 through 249 Processing helix chain 'X' and resid 256 through 268 removed outlier: 3.681A pdb=" N HIS X 262 " --> pdb=" O GLN X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 288 removed outlier: 4.059A pdb=" N SER X 288 " --> pdb=" O LYS X 284 " (cutoff:3.500A) 76 hydrogen bonds defined for protein. 228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 0.30 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 471 1.33 - 1.45: 884 1.45 - 1.57: 1149 1.57 - 1.69: 126 1.69 - 1.81: 6 Bond restraints: 2636 Sorted by residual: bond pdb=" CG LEU X 200 " pdb=" CD1 LEU X 200 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.28e+00 bond pdb=" C3' DA I 74 " pdb=" O3' DA I 74 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" C3' DC I 75 " pdb=" C2' DC I 75 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.13e+00 bond pdb=" C3' DC I 95 " pdb=" C2' DC I 95 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 7.98e-01 bond pdb=" CB MET X 197 " pdb=" CG MET X 197 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.79e-01 ... (remaining 2631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 3771 2.38 - 4.76: 42 4.76 - 7.14: 7 7.14 - 9.53: 1 9.53 - 11.91: 1 Bond angle restraints: 3822 Sorted by residual: angle pdb=" CB MET X 197 " pdb=" CG MET X 197 " pdb=" SD MET X 197 " ideal model delta sigma weight residual 112.70 124.61 -11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CA GLU X 238 " pdb=" CB GLU X 238 " pdb=" CG GLU X 238 " ideal model delta sigma weight residual 114.10 120.61 -6.51 2.00e+00 2.50e-01 1.06e+01 angle pdb=" C3' DT J -88 " pdb=" C2' DT J -88 " pdb=" C1' DT J -88 " ideal model delta sigma weight residual 101.60 97.55 4.05 1.50e+00 4.44e-01 7.31e+00 angle pdb=" CA MET X 197 " pdb=" CB MET X 197 " pdb=" CG MET X 197 " ideal model delta sigma weight residual 114.10 119.03 -4.93 2.00e+00 2.50e-01 6.08e+00 angle pdb=" CA LEU X 200 " pdb=" CB LEU X 200 " pdb=" CG LEU X 200 " ideal model delta sigma weight residual 116.30 124.65 -8.35 3.50e+00 8.16e-02 5.69e+00 ... (remaining 3817 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 30.43: 1083 30.43 - 60.84: 356 60.84 - 91.26: 2 91.26 - 121.68: 0 121.68 - 152.10: 2 Dihedral angle restraints: 1443 sinusoidal: 1038 harmonic: 405 Sorted by residual: dihedral pdb=" C4' DA I 74 " pdb=" C3' DA I 74 " pdb=" O3' DA I 74 " pdb=" P DC I 75 " ideal model delta sinusoidal sigma weight residual 220.00 67.90 152.10 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" C4' DG J -93 " pdb=" C3' DG J -93 " pdb=" O3' DG J -93 " pdb=" P DG J -92 " ideal model delta sinusoidal sigma weight residual 220.00 81.85 138.15 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" CA GLU X 238 " pdb=" C GLU X 238 " pdb=" N ASN X 239 " pdb=" CA ASN X 239 " ideal model delta harmonic sigma weight residual -180.00 -164.72 -15.28 0 5.00e+00 4.00e-02 9.34e+00 ... (remaining 1440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 283 0.030 - 0.060: 109 0.060 - 0.089: 26 0.089 - 0.119: 8 0.119 - 0.149: 4 Chirality restraints: 430 Sorted by residual: chirality pdb=" CG LEU X 190 " pdb=" CB LEU X 190 " pdb=" CD1 LEU X 190 " pdb=" CD2 LEU X 190 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA LEU X 267 " pdb=" N LEU X 267 " pdb=" C LEU X 267 " pdb=" CB LEU X 267 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CG LEU X 217 " pdb=" CB LEU X 217 " pdb=" CD1 LEU X 217 " pdb=" CD2 LEU X 217 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 427 not shown) Planarity restraints: 263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS X 254 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO X 255 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO X 255 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO X 255 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC J -80 " -0.019 2.00e-02 2.50e+03 9.43e-03 2.00e+00 pdb=" N1 DC J -80 " 0.019 2.00e-02 2.50e+03 pdb=" C2 DC J -80 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DC J -80 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DC J -80 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DC J -80 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC J -80 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DC J -80 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC J -80 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP X 277 " -0.011 2.00e-02 2.50e+03 8.31e-03 1.72e+00 pdb=" CG TRP X 277 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP X 277 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP X 277 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP X 277 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP X 277 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP X 277 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP X 277 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP X 277 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP X 277 " -0.000 2.00e-02 2.50e+03 ... (remaining 260 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 531 2.80 - 3.33: 2248 3.33 - 3.85: 4846 3.85 - 4.38: 5302 4.38 - 4.90: 7197 Nonbonded interactions: 20124 Sorted by model distance: nonbonded pdb=" O GLN X 155 " pdb=" OG1 THR X 159 " model vdw 2.277 3.040 nonbonded pdb=" OP2 DA J -87 " pdb=" ND2 ASN X 196 " model vdw 2.302 3.120 nonbonded pdb=" NE ARG X 157 " pdb=" OE2 GLU X 188 " model vdw 2.303 3.120 nonbonded pdb=" NH2 ARG X 157 " pdb=" OE1 GLU X 188 " model vdw 2.305 3.120 nonbonded pdb=" O LEU X 248 " pdb=" NE2 GLN X 251 " model vdw 2.308 3.120 ... (remaining 20119 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 group one per residue 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 3.580 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.000 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:0.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2636 Z= 0.203 Angle : 0.730 11.907 3822 Z= 0.409 Chirality : 0.036 0.149 430 Planarity : 0.005 0.041 263 Dihedral : 28.395 152.096 1177 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.79 % Allowed : 18.90 % Favored : 80.31 % 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 aren not related in a simple way. whole: 0.35 (0.74), residues: 136 helix: 0.74 (0.51), residues: 110 sheet: None (None), residues: 0 loop : -1.73 (1.21), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG X 234 TYR 0.000 0.000 TYR X 162 PHE 0.011 0.002 PHE X 187 TRP 0.022 0.003 TRP X 277 HIS 0.001 0.001 HIS X 262 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 2636) covalent geometry : angle 0.72981 ( 3822) hydrogen bonds : bond 0.06481 ( 150) hydrogen bonds : angle 3.84857 ( 376) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 149 PHE cc_start: 0.6098 (t80) cc_final: 0.5746 (t80) REVERT: X 273 VAL cc_start: 0.8597 (t) cc_final: 0.8031 (t) outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.0607 time to fit residues: 3.1343 Evaluate side-chains 27 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.031192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.023470 restraints weight = 28681.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.024545 restraints weight = 15038.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.025264 restraints weight = 9647.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.025755 restraints weight = 7000.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.026090 restraints weight = 5484.137| |-----------------------------------------------------------------------------| r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2636 Z= 0.171 Angle : 0.609 6.058 3822 Z= 0.364 Chirality : 0.033 0.124 430 Planarity : 0.005 0.035 263 Dihedral : 30.558 149.750 865 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.73), residues: 136 helix: 0.70 (0.50), residues: 110 sheet: None (None), residues: 0 loop : -1.72 (1.20), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG X 242 TYR 0.001 0.000 TYR X 162 PHE 0.030 0.003 PHE X 278 TRP 0.031 0.004 TRP X 277 HIS 0.001 0.001 HIS X 262 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 2636) covalent geometry : angle 0.60863 ( 3822) hydrogen bonds : bond 0.03974 ( 150) hydrogen bonds : angle 3.70172 ( 376) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 147 GLU cc_start: 0.9421 (tt0) cc_final: 0.9206 (mt-10) REVERT: X 278 PHE cc_start: 0.9806 (m-80) cc_final: 0.9164 (m-80) REVERT: X 280 ASN cc_start: 0.9484 (m110) cc_final: 0.9259 (p0) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0755 time to fit residues: 2.3578 Evaluate side-chains 24 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 218 GLN ** 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 = 0.2725 r_free = 0.2725 target = 0.028032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.020672 restraints weight = 30905.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.021630 restraints weight = 16529.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.022258 restraints weight = 10827.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.022679 restraints weight = 7945.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.022979 restraints weight = 6338.206| |-----------------------------------------------------------------------------| r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2636 Z= 0.213 Angle : 0.620 5.162 3822 Z= 0.371 Chirality : 0.033 0.113 430 Planarity : 0.005 0.037 263 Dihedral : 30.909 148.751 865 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.73), residues: 136 helix: 0.64 (0.50), residues: 111 sheet: None (None), residues: 0 loop : -1.25 (1.26), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 275 TYR 0.005 0.001 TYR X 162 PHE 0.021 0.003 PHE X 278 TRP 0.035 0.005 TRP X 277 HIS 0.006 0.004 HIS X 262 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 2636) covalent geometry : angle 0.62023 ( 3822) hydrogen bonds : bond 0.05318 ( 150) hydrogen bonds : angle 3.81348 ( 376) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 147 GLU cc_start: 0.9430 (tt0) cc_final: 0.9176 (mt-10) REVERT: X 197 MET cc_start: 0.9696 (mmp) cc_final: 0.9482 (mmm) REVERT: X 219 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8628 (mt-10) REVERT: X 246 GLU cc_start: 0.9488 (mm-30) cc_final: 0.9223 (mm-30) REVERT: X 278 PHE cc_start: 0.9836 (m-80) cc_final: 0.9543 (m-80) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0528 time to fit residues: 1.5264 Evaluate side-chains 20 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 196 ASN X 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.028970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.021485 restraints weight = 30228.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.022521 restraints weight = 15573.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.023200 restraints weight = 9904.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.023644 restraints weight = 7135.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.023908 restraints weight = 5600.985| |-----------------------------------------------------------------------------| r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2636 Z= 0.171 Angle : 0.606 6.327 3822 Z= 0.360 Chirality : 0.033 0.148 430 Planarity : 0.004 0.024 263 Dihedral : 30.804 150.873 865 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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 aren not related in a simple way. whole: 0.31 (0.73), residues: 136 helix: 0.58 (0.50), residues: 111 sheet: None (None), residues: 0 loop : -1.08 (1.24), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG X 275 TYR 0.001 0.000 TYR X 162 PHE 0.013 0.002 PHE X 187 TRP 0.027 0.006 TRP X 277 HIS 0.001 0.000 HIS X 262 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 2636) covalent geometry : angle 0.60621 ( 3822) hydrogen bonds : bond 0.04136 ( 150) hydrogen bonds : angle 3.67499 ( 376) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 166 ASP cc_start: 0.9733 (m-30) cc_final: 0.9472 (t70) REVERT: X 244 ASN cc_start: 0.9604 (m110) cc_final: 0.9386 (m110) REVERT: X 278 PHE cc_start: 0.9786 (m-80) cc_final: 0.9365 (m-80) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0454 time to fit residues: 1.5054 Evaluate side-chains 19 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.2776 r_free = 0.2776 target = 0.029539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.022548 restraints weight = 31525.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.023586 restraints weight = 15531.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.024248 restraints weight = 9645.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.024704 restraints weight = 6790.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.024947 restraints weight = 5252.501| |-----------------------------------------------------------------------------| r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2636 Z= 0.162 Angle : 0.598 5.109 3822 Z= 0.357 Chirality : 0.033 0.123 430 Planarity : 0.003 0.017 263 Dihedral : 30.771 150.889 865 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.73), residues: 136 helix: 0.79 (0.51), residues: 110 sheet: None (None), residues: 0 loop : -1.10 (1.15), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG X 275 TYR 0.001 0.000 TYR X 162 PHE 0.010 0.002 PHE X 278 TRP 0.036 0.008 TRP X 277 HIS 0.001 0.001 HIS X 262 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 2636) covalent geometry : angle 0.59795 ( 3822) hydrogen bonds : bond 0.03871 ( 150) hydrogen bonds : angle 3.67214 ( 376) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 246 GLU cc_start: 0.9537 (mm-30) cc_final: 0.9281 (mm-30) REVERT: X 278 PHE cc_start: 0.9821 (m-80) cc_final: 0.9557 (m-80) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0509 time to fit residues: 1.6127 Evaluate side-chains 18 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.2781 r_free = 0.2781 target = 0.029793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.022727 restraints weight = 31567.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.023805 restraints weight = 14600.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.024501 restraints weight = 8823.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.024956 restraints weight = 6129.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.025268 restraints weight = 4717.125| |-----------------------------------------------------------------------------| r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2636 Z= 0.159 Angle : 0.596 5.521 3822 Z= 0.359 Chirality : 0.032 0.116 430 Planarity : 0.003 0.014 263 Dihedral : 30.784 151.120 865 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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 aren not related in a simple way. whole: 0.36 (0.73), residues: 136 helix: 0.65 (0.51), residues: 110 sheet: None (None), residues: 0 loop : -1.20 (1.11), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 275 TYR 0.001 0.000 TYR X 162 PHE 0.014 0.002 PHE X 278 TRP 0.030 0.004 TRP X 277 HIS 0.000 0.000 HIS X 262 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 2636) covalent geometry : angle 0.59552 ( 3822) hydrogen bonds : bond 0.03822 ( 150) hydrogen bonds : angle 3.87117 ( 376) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 166 ASP cc_start: 0.9719 (m-30) cc_final: 0.9442 (t70) REVERT: X 246 GLU cc_start: 0.9460 (mm-30) cc_final: 0.9251 (mm-30) REVERT: X 278 PHE cc_start: 0.9733 (m-80) cc_final: 0.9340 (m-80) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0518 time to fit residues: 1.5071 Evaluate side-chains 19 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.0970 chunk 13 optimal weight: 0.0470 overall best weight: 0.5476 ------------------------------------------------------------------------------- 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 = 0.2831 r_free = 0.2831 target = 0.030393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.023068 restraints weight = 31468.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.024182 restraints weight = 14415.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.024888 restraints weight = 8652.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.025319 restraints weight = 6011.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.025636 restraints weight = 4673.804| |-----------------------------------------------------------------------------| r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2636 Z= 0.153 Angle : 0.595 4.808 3822 Z= 0.357 Chirality : 0.033 0.166 430 Planarity : 0.003 0.015 263 Dihedral : 30.794 151.385 865 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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 aren not related in a simple way. whole: 0.14 (0.72), residues: 136 helix: 0.47 (0.51), residues: 111 sheet: None (None), residues: 0 loop : -1.19 (1.00), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 275 TYR 0.002 0.001 TYR X 162 PHE 0.010 0.001 PHE X 187 TRP 0.039 0.007 TRP X 277 HIS 0.000 0.000 HIS X 262 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 2636) covalent geometry : angle 0.59479 ( 3822) hydrogen bonds : bond 0.03602 ( 150) hydrogen bonds : angle 3.87408 ( 376) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 246 GLU cc_start: 0.9561 (mm-30) cc_final: 0.9310 (mm-30) REVERT: X 278 PHE cc_start: 0.9807 (m-80) cc_final: 0.9533 (m-80) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0657 time to fit residues: 1.8017 Evaluate side-chains 16 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 265 GLN ** 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 = 0.2658 r_free = 0.2658 target = 0.026029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2383 r_free = 0.2383 target = 0.019230 restraints weight = 34289.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.020167 restraints weight = 15968.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.020788 restraints weight = 9788.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.021193 restraints weight = 6888.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.021485 restraints weight = 5370.227| |-----------------------------------------------------------------------------| r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2636 Z= 0.254 Angle : 0.688 8.314 3822 Z= 0.405 Chirality : 0.038 0.153 430 Planarity : 0.004 0.029 263 Dihedral : 31.189 150.083 865 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.69), residues: 136 helix: 0.32 (0.49), residues: 109 sheet: None (None), residues: 0 loop : -1.72 (0.91), residues: 27 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG X 234 TYR 0.005 0.001 TYR X 162 PHE 0.013 0.002 PHE X 149 TRP 0.033 0.005 TRP X 277 HIS 0.003 0.002 HIS X 262 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 2636) covalent geometry : angle 0.68819 ( 3822) hydrogen bonds : bond 0.06034 ( 150) hydrogen bonds : angle 4.30708 ( 376) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.079 Fit side-chains revert: symmetry clash REVERT: X 147 GLU cc_start: 0.9412 (tt0) cc_final: 0.9142 (mt-10) REVERT: X 244 ASN cc_start: 0.9631 (m110) cc_final: 0.9425 (m110) REVERT: X 278 PHE cc_start: 0.9824 (m-80) cc_final: 0.9550 (m-80) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0550 time to fit residues: 1.7538 Evaluate side-chains 16 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.2705 r_free = 0.2705 target = 0.027287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.020516 restraints weight = 33837.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.021512 restraints weight = 15656.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.022169 restraints weight = 9548.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.022536 restraints weight = 6691.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.022897 restraints weight = 5322.631| |-----------------------------------------------------------------------------| r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2636 Z= 0.183 Angle : 0.648 5.384 3822 Z= 0.388 Chirality : 0.037 0.179 430 Planarity : 0.003 0.019 263 Dihedral : 31.236 150.211 865 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.69), residues: 136 helix: 0.44 (0.50), residues: 109 sheet: None (None), residues: 0 loop : -1.75 (0.90), residues: 27 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG X 275 TYR 0.001 0.000 TYR X 162 PHE 0.011 0.002 PHE X 187 TRP 0.040 0.009 TRP X 207 HIS 0.001 0.000 HIS X 262 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 2636) covalent geometry : angle 0.64819 ( 3822) hydrogen bonds : bond 0.04547 ( 150) hydrogen bonds : angle 4.27519 ( 376) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.064 Fit side-chains revert: symmetry clash REVERT: X 147 GLU cc_start: 0.9353 (tt0) cc_final: 0.9133 (mt-10) REVERT: X 206 LYS cc_start: 0.9504 (mttm) cc_final: 0.9211 (mtmm) REVERT: X 278 PHE cc_start: 0.9804 (m-80) cc_final: 0.9558 (m-80) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0705 time to fit residues: 1.9913 Evaluate side-chains 17 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.2754 r_free = 0.2754 target = 0.028436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.021385 restraints weight = 34168.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.022373 restraints weight = 15818.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.023005 restraints weight = 9611.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.023403 restraints weight = 6744.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.023689 restraints weight = 5284.709| |-----------------------------------------------------------------------------| r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.5872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2636 Z= 0.169 Angle : 0.631 5.085 3822 Z= 0.378 Chirality : 0.036 0.176 430 Planarity : 0.004 0.021 263 Dihedral : 31.253 150.422 865 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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 aren not related in a simple way. whole: 0.04 (0.71), residues: 136 helix: 0.53 (0.51), residues: 109 sheet: None (None), residues: 0 loop : -1.76 (0.93), residues: 27 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 240 TYR 0.003 0.001 TYR X 162 PHE 0.010 0.001 PHE X 187 TRP 0.038 0.005 TRP X 277 HIS 0.001 0.001 HIS X 262 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 2636) covalent geometry : angle 0.63055 ( 3822) hydrogen bonds : bond 0.04280 ( 150) hydrogen bonds : angle 4.17775 ( 376) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 147 GLU cc_start: 0.9387 (tt0) cc_final: 0.9137 (mt-10) REVERT: X 244 ASN cc_start: 0.9594 (m110) cc_final: 0.9380 (m110) REVERT: X 278 PHE cc_start: 0.9716 (m-80) cc_final: 0.9435 (m-80) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0671 time to fit residues: 1.8071 Evaluate side-chains 17 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.2766 r_free = 0.2766 target = 0.028607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.021713 restraints weight = 32559.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.022751 restraints weight = 15049.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.023423 restraints weight = 9172.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.023805 restraints weight = 6400.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.024115 restraints weight = 5100.972| |-----------------------------------------------------------------------------| r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2636 Z= 0.164 Angle : 0.636 5.104 3822 Z= 0.380 Chirality : 0.036 0.163 430 Planarity : 0.004 0.018 263 Dihedral : 31.273 150.490 865 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.70), residues: 136 helix: 0.37 (0.50), residues: 109 sheet: None (None), residues: 0 loop : -1.81 (0.93), residues: 27 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 275 TYR 0.002 0.000 TYR X 162 PHE 0.011 0.001 PHE X 187 TRP 0.044 0.008 TRP X 207 HIS 0.000 0.000 HIS X 262 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 2636) covalent geometry : angle 0.63604 ( 3822) hydrogen bonds : bond 0.04176 ( 150) hydrogen bonds : angle 4.13126 ( 376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 618.44 seconds wall clock time: 11 minutes 16.67 seconds (676.67 seconds total)