Starting phenix.real_space_refine on Thu Sep 10 20:49:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6m7d_30129/09_2026/6m7d_30129.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m7d_30129/09_2026/6m7d_30129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m7d_30129/09_2026/6m7d_30129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m7d_30129/09_2026/6m7d_30129.map" model { file = "/net/cci-nas-00/data/ceres_data/6m7d_30129/09_2026/6m7d_30129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m7d_30129/09_2026/6m7d_30129.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6m7d_30129/09_2026/6m7d_30129.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6m7d_30129/09_2026/6m7d_30129.cif" } resolution = 2.9 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= 0.006 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 6 5.49 5 S 14 5.16 5 C 2054 2.51 5 N 552 2.21 5 O 654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3280 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3160 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 15, 'TRANS': 396} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'RNAv2': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 1.08, per 1000 atoms: 0.33 Number of scatterers: 3280 At special positions: 0 Unit cell: (78.52, 81.64, 88.4, 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 14 16.00 P 6 15.00 O 654 8.00 N 552 7.00 C 2054 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: 0.27 Conformation dependent library (CDL) restraints added in 102.3 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 67.5% alpha, 5.3% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 46 through 63 Processing helix chain 'A' and resid 67 through 81 Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 128 through 136 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 162 through 182 removed outlier: 4.144A pdb=" N LYS A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 203 removed outlier: 4.224A pdb=" N ALA A 198 " --> pdb=" O ASN A 194 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.763A pdb=" N VAL A 210 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 226 through 240 Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 289 through 306 Processing helix chain 'A' and resid 307 through 313 Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 318 through 328 removed outlier: 4.001A pdb=" N GLY A 322 " --> pdb=" O PRO A 319 " (cutoff:3.500A) Proline residue: A 326 - end of helix Processing helix chain 'A' and resid 329 through 344 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 380 through 385 Processing helix chain 'A' and resid 387 through 402 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 40 removed outlier: 6.533A pdb=" N SER A 33 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL A 102 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 35 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR A 104 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL A 37 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE A 106 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A 39 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N LYS A 108 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 105 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 120 " --> pdb=" O TYR A 127 " (cutoff:3.500A) 185 hydrogen bonds defined for protein. 516 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 0.45 Time building geometry restraints manager: 0.38 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: 683 1.33 - 1.45: 765 1.45 - 1.57: 1863 1.57 - 1.69: 11 1.69 - 1.81: 26 Bond restraints: 3348 Sorted by residual: bond pdb=" N SER A 142 " pdb=" CA SER A 142 " ideal model delta sigma weight residual 1.453 1.488 -0.034 9.20e-03 1.18e+04 1.39e+01 bond pdb=" N VAL A 277 " pdb=" CA VAL A 277 " ideal model delta sigma weight residual 1.452 1.496 -0.044 1.18e-02 7.18e+03 1.37e+01 bond pdb=" N VAL A 99 " pdb=" CA VAL A 99 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.08e-02 8.57e+03 1.24e+01 bond pdb=" N VAL A 95 " pdb=" CA VAL A 95 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.10e-02 8.26e+03 9.85e+00 bond pdb=" N MET A 125 " pdb=" CA MET A 125 " ideal model delta sigma weight residual 1.456 1.491 -0.036 1.22e-02 6.72e+03 8.47e+00 ... (remaining 3343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 3574 1.07 - 2.14: 625 2.14 - 3.22: 298 3.22 - 4.29: 47 4.29 - 5.36: 12 Bond angle restraints: 4556 Sorted by residual: angle pdb=" CA ASP A 405 " pdb=" C ASP A 405 " pdb=" O ASP A 405 " ideal model delta sigma weight residual 122.63 118.22 4.41 1.29e+00 6.01e-01 1.17e+01 angle pdb=" N THR A 272 " pdb=" CA THR A 272 " pdb=" C THR A 272 " ideal model delta sigma weight residual 111.28 107.63 3.65 1.09e+00 8.42e-01 1.12e+01 angle pdb=" C ASN A 241 " pdb=" N THR A 242 " pdb=" CA THR A 242 " ideal model delta sigma weight residual 120.28 124.74 -4.46 1.34e+00 5.57e-01 1.11e+01 angle pdb=" C SER A 402 " pdb=" N GLY A 403 " pdb=" CA GLY A 403 " ideal model delta sigma weight residual 120.00 123.63 -3.63 1.10e+00 8.26e-01 1.09e+01 angle pdb=" CA ARG A 149 " pdb=" C ARG A 149 " pdb=" O ARG A 149 " ideal model delta sigma weight residual 121.56 118.10 3.46 1.09e+00 8.42e-01 1.01e+01 ... (remaining 4551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 1797 17.82 - 35.64: 157 35.64 - 53.46: 34 53.46 - 71.28: 10 71.28 - 89.10: 3 Dihedral angle restraints: 2001 sinusoidal: 823 harmonic: 1178 Sorted by residual: dihedral pdb=" C4' U B 3 " pdb=" C3' U B 3 " pdb=" C2' U B 3 " pdb=" C1' U B 3 " ideal model delta sinusoidal sigma weight residual 36.34 -34.20 70.54 1 3.10e+00 1.04e-01 6.66e+02 dihedral pdb=" O4' U B 3 " pdb=" C4' U B 3 " pdb=" C3' U B 3 " pdb=" C2' U B 3 " ideal model delta sinusoidal sigma weight residual -35.15 21.70 -56.84 1 4.00e+00 6.25e-02 2.72e+02 dihedral pdb=" O4' U B 3 " pdb=" C2' U B 3 " pdb=" C1' U B 3 " pdb=" C3' U B 3 " ideal model delta sinusoidal sigma weight residual -94.41 -35.75 -58.65 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 355 0.066 - 0.132: 139 0.132 - 0.197: 31 0.197 - 0.263: 6 0.263 - 0.329: 2 Chirality restraints: 533 Sorted by residual: chirality pdb=" P U B 1 " pdb=" OP1 U B 1 " pdb=" OP2 U B 1 " pdb=" O5' U B 1 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C2' U B 3 " pdb=" C3' U B 3 " pdb=" O2' U B 3 " pdb=" C1' U B 3 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA GLU A 278 " pdb=" N GLU A 278 " pdb=" C GLU A 278 " pdb=" CB GLU A 278 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 530 not shown) Planarity restraints: 564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B 2 " 0.031 2.00e-02 2.50e+03 1.53e-02 5.25e+00 pdb=" N1 U B 2 " -0.031 2.00e-02 2.50e+03 pdb=" C2 U B 2 " -0.007 2.00e-02 2.50e+03 pdb=" O2 U B 2 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U B 2 " 0.005 2.00e-02 2.50e+03 pdb=" C4 U B 2 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U B 2 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U B 2 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U B 2 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 240 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C MET A 240 " 0.033 2.00e-02 2.50e+03 pdb=" O MET A 240 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN A 241 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 44 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C VAL A 44 " -0.031 2.00e-02 2.50e+03 pdb=" O VAL A 44 " 0.012 2.00e-02 2.50e+03 pdb=" N THR A 45 " 0.010 2.00e-02 2.50e+03 ... (remaining 561 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 115 2.71 - 3.25: 3405 3.25 - 3.80: 5504 3.80 - 4.35: 7360 4.35 - 4.90: 11397 Nonbonded interactions: 27781 Sorted by model distance: nonbonded pdb=" O ALA A 346 " pdb=" O2' U B 4 " model vdw 2.157 3.040 nonbonded pdb=" O THR A 183 " pdb=" O2' U B 2 " model vdw 2.198 3.040 nonbonded pdb=" O ALA A 325 " pdb=" ND2 ASN A 328 " model vdw 2.211 3.120 nonbonded pdb=" NE2 GLN A 173 " pdb=" O LEU A 209 " model vdw 2.220 3.120 nonbonded pdb=" OD2 ASP A 202 " pdb=" OG1 THR A 204 " model vdw 2.262 3.040 ... (remaining 27776 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: 14.240 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: 0.180 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.930 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.020 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:7.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 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 : 0.010 0.056 3348 Z= 0.631 Angle : 1.054 5.361 4556 Z= 0.761 Chirality : 0.074 0.329 533 Planarity : 0.005 0.041 564 Dihedral : 14.529 89.104 1249 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.58 % Allowed : 13.12 % Favored : 86.30 % 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: -0.46 (0.38), residues: 410 helix: -0.14 (0.32), residues: 244 sheet: -0.49 (1.15), residues: 23 loop : -0.28 (0.41), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 195 TYR 0.011 0.002 TYR A 275 PHE 0.016 0.002 PHE A 193 TRP 0.006 0.001 TRP A 333 HIS 0.004 0.001 HIS A 397 Details of bonding type rmsd/Z covalent geometry : bond 0.01003 / 0.63 ( 3348) covalent geometry : angle 1.05402 / 0.76 ( 4556) hydrogen bonds : bond 0.15669 / 10.79 ( 185) hydrogen bonds : angle 7.53487 / 5.11 ( 516) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.149 Fit side-chains REVERT: A 290 ARG cc_start: 0.8141 (ttt180) cc_final: 0.7519 (ttp-110) REVERT: A 400 ASN cc_start: 0.8217 (m-40) cc_final: 0.7949 (m-40) outliers start: 2 outliers final: 1 residues processed: 68 average time/residue: 0.6294 time to fit residues: 43.8157 Evaluate side-chains 49 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.0070 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.0770 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 ASN A 93 ASN ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 ASN A 227 GLN A 241 ASN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 288 ASN A 366 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.148544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.125020 restraints weight = 3487.953| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 0.96 r_work: 0.2987 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3348 Z= 0.119 Angle : 0.543 6.769 4556 Z= 0.270 Chirality : 0.046 0.316 533 Planarity : 0.004 0.032 564 Dihedral : 8.266 118.135 517 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.33 % Allowed : 14.29 % Favored : 83.38 % 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: 0.72 (0.39), residues: 410 helix: 0.78 (0.33), residues: 247 sheet: -0.17 (1.04), residues: 23 loop : 0.31 (0.43), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 395 TYR 0.008 0.001 TYR A 275 PHE 0.013 0.001 PHE A 269 TRP 0.003 0.001 TRP A 333 HIS 0.003 0.001 HIS A 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 3348) covalent geometry : angle 0.54259 / 0.27 ( 4556) hydrogen bonds : bond 0.04795 / 3.30 ( 185) hydrogen bonds : angle 5.50245 / 3.83 ( 516) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.131 Fit side-chains REVERT: A 56 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8437 (p) REVERT: A 62 LEU cc_start: 0.9075 (mt) cc_final: 0.8838 (mm) REVERT: A 290 ARG cc_start: 0.8660 (ttt180) cc_final: 0.7543 (ttp-110) REVERT: A 345 LYS cc_start: 0.8278 (tppt) cc_final: 0.8016 (mmpt) REVERT: A 377 SER cc_start: 0.8836 (p) cc_final: 0.8573 (p) REVERT: A 400 ASN cc_start: 0.8195 (m-40) cc_final: 0.7968 (m-40) outliers start: 8 outliers final: 4 residues processed: 57 average time/residue: 0.5784 time to fit residues: 33.9507 Evaluate side-chains 53 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.146108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.121750 restraints weight = 3348.669| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.16 r_work: 0.2871 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3348 Z= 0.140 Angle : 0.520 6.318 4556 Z= 0.259 Chirality : 0.045 0.261 533 Planarity : 0.003 0.031 564 Dihedral : 8.619 135.468 517 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.92 % Allowed : 14.58 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.40), residues: 410 helix: 1.24 (0.34), residues: 241 sheet: -0.40 (0.94), residues: 25 loop : 1.06 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.006 0.001 TYR A 303 PHE 0.011 0.002 PHE A 269 TRP 0.005 0.001 TRP A 333 HIS 0.003 0.001 HIS A 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 3348) covalent geometry : angle 0.52028 / 0.26 ( 4556) hydrogen bonds : bond 0.04736 / 3.23 ( 185) hydrogen bonds : angle 5.21486 / 3.66 ( 516) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.132 Fit side-chains REVERT: A 56 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8417 (p) REVERT: A 201 GLN cc_start: 0.6445 (OUTLIER) cc_final: 0.5900 (tt0) REVERT: A 290 ARG cc_start: 0.8774 (ttt180) cc_final: 0.7631 (ttp-110) REVERT: A 345 LYS cc_start: 0.8309 (tppt) cc_final: 0.8080 (mmpt) REVERT: A 377 SER cc_start: 0.8908 (p) cc_final: 0.8638 (p) REVERT: A 400 ASN cc_start: 0.8294 (m-40) cc_final: 0.8042 (m-40) outliers start: 10 outliers final: 4 residues processed: 52 average time/residue: 0.6182 time to fit residues: 33.0256 Evaluate side-chains 45 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.144601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.119740 restraints weight = 3375.569| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.24 r_work: 0.2857 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3348 Z= 0.181 Angle : 0.552 7.016 4556 Z= 0.273 Chirality : 0.047 0.295 533 Planarity : 0.003 0.030 564 Dihedral : 8.675 133.881 517 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.92 % Allowed : 14.58 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.40), residues: 410 helix: 1.18 (0.34), residues: 240 sheet: -0.30 (0.91), residues: 25 loop : 1.11 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.007 0.001 TYR A 303 PHE 0.010 0.002 PHE A 193 TRP 0.005 0.001 TRP A 333 HIS 0.003 0.001 HIS A 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 3348) covalent geometry : angle 0.55167 / 0.27 ( 4556) hydrogen bonds : bond 0.05051 / 3.46 ( 185) hydrogen bonds : angle 5.25458 / 3.70 ( 516) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.075 Fit side-chains REVERT: A 201 GLN cc_start: 0.6485 (OUTLIER) cc_final: 0.5944 (tt0) REVERT: A 290 ARG cc_start: 0.8624 (ttt180) cc_final: 0.7594 (ttp-110) REVERT: A 400 ASN cc_start: 0.8156 (m-40) cc_final: 0.7883 (m-40) outliers start: 10 outliers final: 6 residues processed: 49 average time/residue: 0.5976 time to fit residues: 30.1840 Evaluate side-chains 44 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.145497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.121449 restraints weight = 3399.474| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.05 r_work: 0.2922 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3348 Z= 0.145 Angle : 0.519 7.031 4556 Z= 0.257 Chirality : 0.046 0.297 533 Planarity : 0.003 0.030 564 Dihedral : 8.627 132.802 517 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.92 % Allowed : 14.29 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.41), residues: 410 helix: 1.27 (0.34), residues: 240 sheet: -0.21 (0.91), residues: 25 loop : 1.23 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.006 0.001 TYR A 303 PHE 0.011 0.002 PHE A 269 TRP 0.005 0.001 TRP A 333 HIS 0.003 0.001 HIS A 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 3348) covalent geometry : angle 0.51922 / 0.26 ( 4556) hydrogen bonds : bond 0.04667 / 3.19 ( 185) hydrogen bonds : angle 5.10121 / 3.60 ( 516) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.144 Fit side-chains REVERT: A 201 GLN cc_start: 0.6480 (OUTLIER) cc_final: 0.5874 (tt0) REVERT: A 290 ARG cc_start: 0.8763 (ttt180) cc_final: 0.7631 (ttp-110) REVERT: A 400 ASN cc_start: 0.8198 (m-40) cc_final: 0.7948 (m-40) outliers start: 10 outliers final: 6 residues processed: 48 average time/residue: 0.5423 time to fit residues: 26.8501 Evaluate side-chains 45 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.147845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.124037 restraints weight = 3401.119| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 0.98 r_work: 0.2870 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3348 Z= 0.116 Angle : 0.514 8.834 4556 Z= 0.247 Chirality : 0.045 0.288 533 Planarity : 0.003 0.030 564 Dihedral : 8.536 131.562 517 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.92 % Allowed : 14.87 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.41), residues: 410 helix: 1.41 (0.34), residues: 242 sheet: -0.09 (0.88), residues: 25 loop : 1.35 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 395 TYR 0.006 0.001 TYR A 275 PHE 0.011 0.001 PHE A 269 TRP 0.004 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 3348) covalent geometry : angle 0.51357 / 0.25 ( 4556) hydrogen bonds : bond 0.04288 / 2.93 ( 185) hydrogen bonds : angle 4.91917 / 3.48 ( 516) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.160 Fit side-chains REVERT: A 56 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8437 (p) REVERT: A 201 GLN cc_start: 0.6395 (OUTLIER) cc_final: 0.5832 (tt0) REVERT: A 290 ARG cc_start: 0.8630 (ttt180) cc_final: 0.7580 (ttp-110) REVERT: A 400 ASN cc_start: 0.8161 (m-40) cc_final: 0.7924 (m-40) outliers start: 10 outliers final: 6 residues processed: 55 average time/residue: 0.5175 time to fit residues: 29.3979 Evaluate side-chains 48 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.145174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.120935 restraints weight = 3434.023| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.19 r_work: 0.2809 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3348 Z= 0.165 Angle : 0.549 7.308 4556 Z= 0.266 Chirality : 0.047 0.282 533 Planarity : 0.003 0.029 564 Dihedral : 8.648 133.925 517 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.62 % Allowed : 15.74 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.41), residues: 410 helix: 1.37 (0.34), residues: 239 sheet: 0.11 (0.91), residues: 25 loop : 1.35 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 14 TYR 0.009 0.001 TYR A 127 PHE 0.009 0.002 PHE A 193 TRP 0.005 0.001 TRP A 333 HIS 0.002 0.001 HIS A 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 3348) covalent geometry : angle 0.54908 / 0.27 ( 4556) hydrogen bonds : bond 0.04847 / 3.31 ( 185) hydrogen bonds : angle 5.06802 / 3.58 ( 516) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.128 Fit side-chains REVERT: A 201 GLN cc_start: 0.6447 (OUTLIER) cc_final: 0.5893 (tt0) REVERT: A 290 ARG cc_start: 0.8673 (ttt180) cc_final: 0.7617 (ttp-110) REVERT: A 400 ASN cc_start: 0.8239 (m-40) cc_final: 0.7968 (m-40) outliers start: 9 outliers final: 7 residues processed: 48 average time/residue: 0.5407 time to fit residues: 26.7969 Evaluate side-chains 47 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.148593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.125150 restraints weight = 3462.652| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.07 r_work: 0.2949 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3348 Z= 0.114 Angle : 0.511 7.112 4556 Z= 0.246 Chirality : 0.045 0.294 533 Planarity : 0.003 0.030 564 Dihedral : 8.531 131.238 517 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.62 % Allowed : 15.74 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.41), residues: 410 helix: 1.47 (0.34), residues: 242 sheet: 0.28 (0.91), residues: 25 loop : 1.30 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 395 TYR 0.006 0.001 TYR A 275 PHE 0.012 0.001 PHE A 269 TRP 0.004 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 3348) covalent geometry : angle 0.51083 / 0.25 ( 4556) hydrogen bonds : bond 0.04222 / 2.89 ( 185) hydrogen bonds : angle 4.84352 / 3.44 ( 516) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.179 Fit side-chains REVERT: A 56 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8425 (p) REVERT: A 201 GLN cc_start: 0.6341 (OUTLIER) cc_final: 0.5760 (tt0) REVERT: A 290 ARG cc_start: 0.8707 (ttt180) cc_final: 0.7598 (ttp-110) REVERT: A 400 ASN cc_start: 0.8210 (m-40) cc_final: 0.7960 (m-40) outliers start: 9 outliers final: 6 residues processed: 49 average time/residue: 0.5783 time to fit residues: 29.1949 Evaluate side-chains 51 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.145101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.121060 restraints weight = 3409.612| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.13 r_work: 0.2833 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3348 Z= 0.169 Angle : 0.559 7.229 4556 Z= 0.271 Chirality : 0.047 0.280 533 Planarity : 0.003 0.029 564 Dihedral : 8.644 133.977 517 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.33 % Allowed : 16.33 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.41), residues: 410 helix: 1.36 (0.34), residues: 239 sheet: 0.27 (0.91), residues: 25 loop : 1.34 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 395 TYR 0.008 0.001 TYR A 127 PHE 0.010 0.002 PHE A 193 TRP 0.005 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 3348) covalent geometry : angle 0.55904 / 0.27 ( 4556) hydrogen bonds : bond 0.04864 / 3.32 ( 185) hydrogen bonds : angle 5.05361 / 3.58 ( 516) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.110 Fit side-chains REVERT: A 290 ARG cc_start: 0.8644 (ttt180) cc_final: 0.7586 (ttp-110) REVERT: A 400 ASN cc_start: 0.8244 (m-40) cc_final: 0.7951 (m-40) outliers start: 8 outliers final: 7 residues processed: 48 average time/residue: 0.5984 time to fit residues: 29.5965 Evaluate side-chains 46 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 389 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 0.0770 chunk 0 optimal weight: 7.9990 chunk 32 optimal weight: 0.0370 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.151616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.128539 restraints weight = 3403.576| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.19 r_work: 0.2924 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3348 Z= 0.100 Angle : 0.510 7.433 4556 Z= 0.245 Chirality : 0.044 0.287 533 Planarity : 0.003 0.030 564 Dihedral : 8.384 128.969 517 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.04 % Allowed : 16.91 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.41), residues: 410 helix: 1.61 (0.34), residues: 242 sheet: 0.36 (0.90), residues: 25 loop : 1.33 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 395 TYR 0.008 0.001 TYR A 275 PHE 0.014 0.001 PHE A 269 TRP 0.003 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 ( 3348) covalent geometry : angle 0.51022 / 0.25 ( 4556) hydrogen bonds : bond 0.03881 / 2.64 ( 185) hydrogen bonds : angle 4.70229 / 3.37 ( 516) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.134 Fit side-chains REVERT: A 280 LYS cc_start: 0.8725 (mttt) cc_final: 0.8412 (mttm) REVERT: A 290 ARG cc_start: 0.8616 (ttt180) cc_final: 0.7584 (ttp-110) REVERT: A 400 ASN cc_start: 0.8156 (m-40) cc_final: 0.7921 (m-40) outliers start: 7 outliers final: 5 residues processed: 51 average time/residue: 0.4959 time to fit residues: 26.1509 Evaluate side-chains 46 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 35 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.0270 chunk 10 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 overall best weight: 0.8642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.150196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.126330 restraints weight = 3441.392| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.11 r_work: 0.2906 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3348 Z= 0.108 Angle : 0.517 7.625 4556 Z= 0.250 Chirality : 0.044 0.250 533 Planarity : 0.003 0.030 564 Dihedral : 8.404 131.654 517 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.46 % Allowed : 18.66 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.41), residues: 410 helix: 1.69 (0.34), residues: 242 sheet: 0.46 (0.90), residues: 25 loop : 1.37 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 395 TYR 0.011 0.001 TYR A 127 PHE 0.013 0.001 PHE A 269 TRP 0.004 0.001 TRP A 333 HIS 0.002 0.001 HIS A 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 3348) covalent geometry : angle 0.51674 / 0.25 ( 4556) hydrogen bonds : bond 0.04108 / 2.79 ( 185) hydrogen bonds : angle 4.72071 / 3.39 ( 516) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1639.69 seconds wall clock time: 28 minutes 51.36 seconds (1731.36 seconds total)