Starting phenix.real_space_refine on Wed Sep 17 03:00:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ei2_48074/09_2025/9ei2_48074.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ei2_48074/09_2025/9ei2_48074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ei2_48074/09_2025/9ei2_48074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ei2_48074/09_2025/9ei2_48074.map" model { file = "/net/cci-nas-00/data/ceres_data/9ei2_48074/09_2025/9ei2_48074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ei2_48074/09_2025/9ei2_48074.cif" } resolution = 2.8 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= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 1353 2.51 5 N 388 2.21 5 O 427 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2182 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1177 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "U" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1005 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 6, 'TRANS': 116} Time building chain proxies: 1.10, per 1000 atoms: 0.50 Number of scatterers: 2182 At special positions: 0 Unit cell: (74.55, 56.7, 68.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 427 8.00 N 388 7.00 C 1353 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: 0.20 Conformation dependent library (CDL) restraints added in 104.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 524 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 1 sheets defined 49.4% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 1165 through 1168 Processing helix chain 'A' and resid 1189 through 1198 removed outlier: 3.670A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.580A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1280 through 1295 removed outlier: 3.567A pdb=" N PHE A1284 " --> pdb=" O ASP A1280 " (cutoff:3.500A) Processing helix chain 'U' and resid 499 through 514 Processing helix chain 'U' and resid 546 through 567 Processing helix chain 'U' and resid 573 through 591 removed outlier: 4.237A pdb=" N ARG U 577 " --> pdb=" O GLU U 573 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA U 578 " --> pdb=" O ALA U 574 " (cutoff:3.500A) Processing helix chain 'U' and resid 593 through 615 Processing sheet with id=AA1, first strand: chain 'A' and resid 1170 through 1177 removed outlier: 7.300A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) 105 hydrogen bonds defined for protein. 312 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.31 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 757 1.34 - 1.46: 383 1.46 - 1.58: 1052 1.58 - 1.70: 0 1.70 - 1.81: 24 Bond restraints: 2216 Sorted by residual: bond pdb=" CB GLN U 566 " pdb=" CG GLN U 566 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" CA THR A1297 " pdb=" CB THR A1297 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.48e-01 bond pdb=" CG MET A1279 " pdb=" SD MET A1279 " ideal model delta sigma weight residual 1.803 1.783 0.020 2.50e-02 1.60e+03 6.14e-01 bond pdb=" CB PRO U 533 " pdb=" CG PRO U 533 " ideal model delta sigma weight residual 1.492 1.531 -0.039 5.00e-02 4.00e+02 6.08e-01 bond pdb=" SD MET A1279 " pdb=" CE MET A1279 " ideal model delta sigma weight residual 1.791 1.773 0.018 2.50e-02 1.60e+03 5.07e-01 ... (remaining 2211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 2847 1.16 - 2.31: 102 2.31 - 3.47: 26 3.47 - 4.63: 8 4.63 - 5.79: 3 Bond angle restraints: 2986 Sorted by residual: angle pdb=" C LYS U 521 " pdb=" N ILE U 522 " pdb=" CA ILE U 522 " ideal model delta sigma weight residual 121.97 127.31 -5.34 1.80e+00 3.09e-01 8.79e+00 angle pdb=" CA GLN U 566 " pdb=" CB GLN U 566 " pdb=" CG GLN U 566 " ideal model delta sigma weight residual 114.10 119.89 -5.79 2.00e+00 2.50e-01 8.37e+00 angle pdb=" N ILE U 522 " pdb=" CA ILE U 522 " pdb=" C ILE U 522 " ideal model delta sigma weight residual 109.34 115.03 -5.69 2.08e+00 2.31e-01 7.49e+00 angle pdb=" CB GLN U 566 " pdb=" CG GLN U 566 " pdb=" CD GLN U 566 " ideal model delta sigma weight residual 112.60 116.38 -3.78 1.70e+00 3.46e-01 4.95e+00 angle pdb=" C MET A1296 " pdb=" N THR A1297 " pdb=" CA THR A1297 " ideal model delta sigma weight residual 121.54 125.45 -3.91 1.91e+00 2.74e-01 4.19e+00 ... (remaining 2981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 1120 16.70 - 33.39: 175 33.39 - 50.09: 73 50.09 - 66.78: 21 66.78 - 83.48: 4 Dihedral angle restraints: 1393 sinusoidal: 597 harmonic: 796 Sorted by residual: dihedral pdb=" CA ASP A1280 " pdb=" C ASP A1280 " pdb=" N ASP A1281 " pdb=" CA ASP A1281 " ideal model delta harmonic sigma weight residual -180.00 -160.13 -19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CG LYS A1268 " pdb=" CD LYS A1268 " pdb=" CE LYS A1268 " pdb=" NZ LYS A1268 " ideal model delta sinusoidal sigma weight residual 60.00 119.64 -59.64 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LYS A1225 " pdb=" CA LYS A1225 " pdb=" CB LYS A1225 " pdb=" CG LYS A1225 " ideal model delta sinusoidal sigma weight residual -60.00 -118.87 58.87 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 1390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 205 0.028 - 0.055: 66 0.055 - 0.083: 34 0.083 - 0.111: 19 0.111 - 0.138: 4 Chirality restraints: 328 Sorted by residual: chirality pdb=" CA ILE A1246 " pdb=" N ILE A1246 " pdb=" C ILE A1246 " pdb=" CB ILE A1246 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA THR A1297 " pdb=" N THR A1297 " pdb=" C THR A1297 " pdb=" CB THR A1297 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ILE U 542 " pdb=" N ILE U 542 " pdb=" C ILE U 542 " pdb=" CB ILE U 542 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 325 not shown) Planarity restraints: 395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A1279 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" C MET A1279 " -0.032 2.00e-02 2.50e+03 pdb=" O MET A1279 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP A1280 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A1178 " -0.018 5.00e-02 4.00e+02 2.70e-02 1.17e+00 pdb=" N PRO A1179 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A1179 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A1179 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A1184 " 0.005 2.00e-02 2.50e+03 1.02e-02 1.03e+00 pdb=" C THR A1184 " -0.018 2.00e-02 2.50e+03 pdb=" O THR A1184 " 0.007 2.00e-02 2.50e+03 pdb=" N VAL A1185 " 0.006 2.00e-02 2.50e+03 ... (remaining 392 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 63 2.70 - 3.25: 2174 3.25 - 3.80: 3602 3.80 - 4.35: 4325 4.35 - 4.90: 7184 Nonbonded interactions: 17348 Sorted by model distance: nonbonded pdb=" O PRO A1181 " pdb=" OG1 THR A1184 " model vdw 2.155 3.040 nonbonded pdb=" OE2 GLU U 584 " pdb=" OH TYR U 597 " model vdw 2.191 3.040 nonbonded pdb=" NH2 ARG U 550 " pdb=" OE1 GLU U 584 " model vdw 2.209 3.120 nonbonded pdb=" NH2 ARG U 541 " pdb=" O ALA U 591 " model vdw 2.271 3.120 nonbonded pdb=" OG1 THR U 587 " pdb=" NZ LYS U 604 " model vdw 2.334 3.120 ... (remaining 17343 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: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.070 Find NCS groups from input model: 0.020 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:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 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 0.039 2216 Z= 0.155 Angle : 0.577 5.787 2986 Z= 0.316 Chirality : 0.041 0.138 328 Planarity : 0.004 0.036 395 Dihedral : 19.853 83.479 869 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.60 % Favored : 91.63 % Rotamer: Outliers : 4.96 % Allowed : 31.40 % Favored : 63.64 % 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: -0.10 (0.53), residues: 263 helix: 1.63 (0.48), residues: 129 sheet: -0.84 (0.77), residues: 28 loop : -2.09 (0.60), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 577 TYR 0.009 0.002 TYR U 508 PHE 0.011 0.002 PHE A1247 TRP 0.007 0.001 TRP A1192 HIS 0.002 0.001 HIS U 552 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 2216) covalent geometry : angle 0.57652 ( 2986) hydrogen bonds : bond 0.10374 ( 105) hydrogen bonds : angle 5.05804 ( 312) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.090 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 12 residues processed: 71 average time/residue: 0.5628 time to fit residues: 40.7363 Evaluate side-chains 71 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1207 ILE Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1267 ASN Chi-restraints excluded: chain A residue 1268 LYS Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1305 SER Chi-restraints excluded: chain U residue 516 LYS Chi-restraints excluded: chain U residue 518 LYS Chi-restraints excluded: chain U residue 519 ASP Chi-restraints excluded: chain U residue 522 ILE Chi-restraints excluded: chain U residue 545 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.0270 chunk 18 optimal weight: 0.9990 overall best weight: 0.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.154349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.127948 restraints weight = 3140.245| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.19 r_work: 0.3499 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2216 Z= 0.141 Angle : 0.546 6.114 2986 Z= 0.289 Chirality : 0.042 0.150 328 Planarity : 0.004 0.028 395 Dihedral : 7.724 57.624 320 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.60 % Favored : 91.63 % Rotamer: Outliers : 8.68 % Allowed : 26.45 % Favored : 64.88 % 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 aren not related in a simple way. whole: 0.27 (0.54), residues: 263 helix: 2.01 (0.48), residues: 129 sheet: -0.90 (0.72), residues: 28 loop : -1.93 (0.62), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG U 577 TYR 0.011 0.002 TYR A1176 PHE 0.011 0.002 PHE A1247 TRP 0.010 0.001 TRP A1192 HIS 0.002 0.001 HIS U 552 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 2216) covalent geometry : angle 0.54599 ( 2986) hydrogen bonds : bond 0.03386 ( 105) hydrogen bonds : angle 4.20467 ( 312) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1167 ARG cc_start: 0.8578 (ttm-80) cc_final: 0.8347 (ttt90) REVERT: A 1270 GLN cc_start: 0.5834 (OUTLIER) cc_final: 0.5543 (tm-30) REVERT: A 1296 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.8000 (tpp) outliers start: 21 outliers final: 10 residues processed: 77 average time/residue: 0.6203 time to fit residues: 48.6034 Evaluate side-chains 77 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1188 GLU Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1270 GLN Chi-restraints excluded: chain A residue 1280 ASP Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain U residue 509 GLN Chi-restraints excluded: chain U residue 512 MET Chi-restraints excluded: chain U residue 545 LEU Chi-restraints excluded: chain U residue 568 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.0870 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.153234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.125446 restraints weight = 3136.807| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.25 r_work: 0.3492 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2216 Z= 0.150 Angle : 0.550 5.883 2986 Z= 0.291 Chirality : 0.042 0.165 328 Planarity : 0.004 0.031 395 Dihedral : 5.334 33.470 297 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.60 % Favored : 91.63 % Rotamer: Outliers : 4.96 % Allowed : 28.51 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.54), residues: 263 helix: 1.90 (0.48), residues: 130 sheet: -0.89 (0.71), residues: 28 loop : -2.02 (0.60), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1218 TYR 0.010 0.001 TYR A1197 PHE 0.012 0.002 PHE A1247 TRP 0.006 0.001 TRP A1192 HIS 0.002 0.001 HIS U 552 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 2216) covalent geometry : angle 0.55034 ( 2986) hydrogen bonds : bond 0.03382 ( 105) hydrogen bonds : angle 4.09862 ( 312) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1167 ARG cc_start: 0.8592 (ttm-80) cc_final: 0.8221 (ttt-90) REVERT: A 1296 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7978 (tpp) outliers start: 12 outliers final: 8 residues processed: 70 average time/residue: 0.6238 time to fit residues: 44.4602 Evaluate side-chains 74 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1188 GLU Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain U residue 509 GLN Chi-restraints excluded: chain U residue 518 LYS Chi-restraints excluded: chain U residue 545 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.153405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.126656 restraints weight = 3071.522| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.16 r_work: 0.3487 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2216 Z= 0.155 Angle : 0.550 5.896 2986 Z= 0.291 Chirality : 0.042 0.159 328 Planarity : 0.004 0.031 395 Dihedral : 5.339 33.670 297 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.60 % Favored : 91.63 % Rotamer: Outliers : 6.20 % Allowed : 28.93 % Favored : 64.88 % 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 aren not related in a simple way. whole: 0.15 (0.53), residues: 263 helix: 1.80 (0.47), residues: 131 sheet: -0.80 (0.72), residues: 28 loop : -1.97 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1218 TYR 0.013 0.002 TYR A1176 PHE 0.011 0.001 PHE A1247 TRP 0.006 0.001 TRP A1192 HIS 0.002 0.001 HIS U 552 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 2216) covalent geometry : angle 0.55011 ( 2986) hydrogen bonds : bond 0.03357 ( 105) hydrogen bonds : angle 4.04120 ( 312) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1167 ARG cc_start: 0.8591 (ttm-80) cc_final: 0.8362 (ttt90) REVERT: A 1182 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.6955 (mm-40) REVERT: A 1270 GLN cc_start: 0.5815 (OUTLIER) cc_final: 0.5538 (tm-30) REVERT: A 1296 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7946 (tpp) outliers start: 15 outliers final: 6 residues processed: 75 average time/residue: 0.5619 time to fit residues: 42.9433 Evaluate side-chains 76 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1182 GLN Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1270 GLN Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain U residue 509 GLN Chi-restraints excluded: chain U residue 518 LYS Chi-restraints excluded: chain U residue 545 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 20 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.156996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.129420 restraints weight = 3139.089| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.25 r_work: 0.3483 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2216 Z= 0.141 Angle : 0.537 5.829 2986 Z= 0.284 Chirality : 0.041 0.139 328 Planarity : 0.003 0.030 395 Dihedral : 5.019 33.855 295 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.84 % Favored : 92.40 % Rotamer: Outliers : 4.96 % Allowed : 30.99 % Favored : 64.05 % 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 aren not related in a simple way. whole: 0.13 (0.53), residues: 263 helix: 1.78 (0.47), residues: 131 sheet: -0.86 (0.72), residues: 28 loop : -1.93 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1218 TYR 0.009 0.001 TYR A1197 PHE 0.011 0.001 PHE A1247 TRP 0.006 0.001 TRP A1192 HIS 0.002 0.001 HIS U 585 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 2216) covalent geometry : angle 0.53696 ( 2986) hydrogen bonds : bond 0.03279 ( 105) hydrogen bonds : angle 4.05199 ( 312) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1167 ARG cc_start: 0.8605 (ttm-80) cc_final: 0.8372 (ttt90) REVERT: A 1182 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.6921 (mm-40) REVERT: A 1270 GLN cc_start: 0.5830 (OUTLIER) cc_final: 0.5547 (tm-30) REVERT: A 1296 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7981 (tpp) REVERT: U 514 LEU cc_start: 0.8346 (mt) cc_final: 0.8002 (mp) outliers start: 12 outliers final: 6 residues processed: 73 average time/residue: 0.5589 time to fit residues: 41.5528 Evaluate side-chains 76 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1182 GLN Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1270 GLN Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain U residue 509 GLN Chi-restraints excluded: chain U residue 545 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.0000 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.153365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.125821 restraints weight = 3059.463| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.22 r_work: 0.3497 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2216 Z= 0.123 Angle : 0.527 5.862 2986 Z= 0.279 Chirality : 0.041 0.163 328 Planarity : 0.003 0.029 395 Dihedral : 4.952 34.423 295 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.22 % Favored : 92.02 % Rotamer: Outliers : 4.55 % Allowed : 32.23 % Favored : 63.22 % 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 aren not related in a simple way. whole: 0.17 (0.53), residues: 263 helix: 1.77 (0.47), residues: 131 sheet: -0.77 (0.73), residues: 28 loop : -1.87 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1218 TYR 0.014 0.002 TYR A1176 PHE 0.011 0.001 PHE A1247 TRP 0.006 0.001 TRP U 504 HIS 0.002 0.001 HIS U 585 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 2216) covalent geometry : angle 0.52720 ( 2986) hydrogen bonds : bond 0.03110 ( 105) hydrogen bonds : angle 3.98741 ( 312) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1167 ARG cc_start: 0.8603 (ttm-80) cc_final: 0.8245 (ttt-90) REVERT: A 1270 GLN cc_start: 0.5821 (OUTLIER) cc_final: 0.5536 (tm-30) REVERT: A 1296 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7878 (tpp) REVERT: A 1297 THR cc_start: 0.8063 (t) cc_final: 0.7830 (t) outliers start: 11 outliers final: 7 residues processed: 70 average time/residue: 0.5273 time to fit residues: 37.5721 Evaluate side-chains 74 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1270 GLN Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain U residue 509 GLN Chi-restraints excluded: chain U residue 518 LYS Chi-restraints excluded: chain U residue 545 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 20 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 1 optimal weight: 0.0060 chunk 22 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.154159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.127532 restraints weight = 3059.361| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.14 r_work: 0.3496 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2216 Z= 0.132 Angle : 0.541 5.846 2986 Z= 0.286 Chirality : 0.041 0.161 328 Planarity : 0.003 0.029 395 Dihedral : 4.935 34.623 295 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.22 % Favored : 92.02 % Rotamer: Outliers : 5.79 % Allowed : 30.17 % Favored : 64.05 % 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 aren not related in a simple way. whole: 0.15 (0.53), residues: 263 helix: 1.75 (0.47), residues: 131 sheet: -0.75 (0.73), residues: 28 loop : -1.89 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1218 TYR 0.008 0.001 TYR A1197 PHE 0.011 0.001 PHE A1247 TRP 0.006 0.001 TRP U 504 HIS 0.002 0.001 HIS U 585 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 2216) covalent geometry : angle 0.54083 ( 2986) hydrogen bonds : bond 0.03111 ( 105) hydrogen bonds : angle 4.00464 ( 312) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1167 ARG cc_start: 0.8590 (ttm-80) cc_final: 0.8229 (ttt-90) REVERT: A 1182 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.6898 (mm-40) REVERT: A 1270 GLN cc_start: 0.5841 (OUTLIER) cc_final: 0.5538 (tm-30) REVERT: A 1296 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7942 (tpp) outliers start: 14 outliers final: 8 residues processed: 73 average time/residue: 0.5001 time to fit residues: 37.2150 Evaluate side-chains 76 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1182 GLN Chi-restraints excluded: chain A residue 1188 GLU Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1270 GLN Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain U residue 509 GLN Chi-restraints excluded: chain U residue 518 LYS Chi-restraints excluded: chain U residue 545 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 0.0770 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.155729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.127802 restraints weight = 3045.800| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.23 r_work: 0.3487 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2216 Z= 0.135 Angle : 0.568 5.862 2986 Z= 0.302 Chirality : 0.043 0.247 328 Planarity : 0.003 0.028 395 Dihedral : 4.917 34.742 295 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.22 % Favored : 92.02 % Rotamer: Outliers : 4.96 % Allowed : 31.82 % Favored : 63.22 % 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 aren not related in a simple way. whole: 0.13 (0.53), residues: 263 helix: 1.71 (0.47), residues: 131 sheet: -0.71 (0.75), residues: 28 loop : -1.89 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1218 TYR 0.015 0.002 TYR A1176 PHE 0.011 0.001 PHE A1247 TRP 0.006 0.001 TRP A1192 HIS 0.002 0.001 HIS U 585 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 2216) covalent geometry : angle 0.56765 ( 2986) hydrogen bonds : bond 0.03117 ( 105) hydrogen bonds : angle 3.99669 ( 312) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1167 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.8365 (ttt90) REVERT: A 1182 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.6880 (mm-40) REVERT: A 1270 GLN cc_start: 0.5819 (OUTLIER) cc_final: 0.5516 (tm-30) REVERT: A 1296 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7924 (tpp) outliers start: 12 outliers final: 8 residues processed: 67 average time/residue: 0.4464 time to fit residues: 30.4667 Evaluate side-chains 72 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1182 GLN Chi-restraints excluded: chain A residue 1188 GLU Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1270 GLN Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain U residue 509 GLN Chi-restraints excluded: chain U residue 518 LYS Chi-restraints excluded: chain U residue 545 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.0770 chunk 1 optimal weight: 0.0470 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.155989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.127715 restraints weight = 3118.391| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.29 r_work: 0.3494 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2216 Z= 0.122 Angle : 0.559 5.861 2986 Z= 0.298 Chirality : 0.043 0.245 328 Planarity : 0.003 0.028 395 Dihedral : 4.883 35.087 295 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.84 % Favored : 92.40 % Rotamer: Outliers : 4.55 % Allowed : 32.23 % Favored : 63.22 % 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 aren not related in a simple way. whole: 0.12 (0.53), residues: 263 helix: 1.70 (0.47), residues: 131 sheet: -0.72 (0.75), residues: 28 loop : -1.87 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1218 TYR 0.013 0.001 TYR A1176 PHE 0.010 0.001 PHE A1247 TRP 0.006 0.001 TRP U 504 HIS 0.002 0.000 HIS U 585 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 2216) covalent geometry : angle 0.55948 ( 2986) hydrogen bonds : bond 0.03011 ( 105) hydrogen bonds : angle 3.98030 ( 312) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1167 ARG cc_start: 0.8609 (ttm-80) cc_final: 0.8251 (ttt-90) REVERT: A 1182 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.6869 (mm-40) REVERT: A 1270 GLN cc_start: 0.5842 (OUTLIER) cc_final: 0.5539 (tm-30) REVERT: A 1296 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7891 (tpp) outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 0.4921 time to fit residues: 34.5246 Evaluate side-chains 74 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1182 GLN Chi-restraints excluded: chain A residue 1188 GLU Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1270 GLN Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain U residue 509 GLN Chi-restraints excluded: chain U residue 518 LYS Chi-restraints excluded: chain U residue 545 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.155961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.128171 restraints weight = 3094.477| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.21 r_work: 0.3491 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2216 Z= 0.133 Angle : 0.562 5.868 2986 Z= 0.299 Chirality : 0.042 0.139 328 Planarity : 0.003 0.028 395 Dihedral : 4.889 35.128 295 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.22 % Favored : 92.02 % Rotamer: Outliers : 5.37 % Allowed : 30.17 % Favored : 64.46 % 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 (0.53), residues: 263 helix: 1.65 (0.47), residues: 131 sheet: -0.70 (0.76), residues: 28 loop : -1.89 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1260 TYR 0.008 0.001 TYR A1197 PHE 0.010 0.001 PHE A1247 TRP 0.006 0.001 TRP A1192 HIS 0.002 0.001 HIS U 585 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 2216) covalent geometry : angle 0.56228 ( 2986) hydrogen bonds : bond 0.03061 ( 105) hydrogen bonds : angle 4.04497 ( 312) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 526 Ramachandran restraints generated. 263 Oldfield, 0 Emsley, 263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1167 ARG cc_start: 0.8601 (ttm-80) cc_final: 0.8368 (ttt90) REVERT: A 1182 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.6873 (mm-40) REVERT: A 1270 GLN cc_start: 0.5870 (OUTLIER) cc_final: 0.5570 (tm-30) REVERT: A 1296 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7954 (tpp) REVERT: U 514 LEU cc_start: 0.8332 (mt) cc_final: 0.8115 (mp) REVERT: U 565 ARG cc_start: 0.5992 (OUTLIER) cc_final: 0.5641 (mmm-85) outliers start: 13 outliers final: 7 residues processed: 70 average time/residue: 0.5383 time to fit residues: 38.3542 Evaluate side-chains 75 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1182 GLN Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1221 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1270 GLN Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain U residue 509 GLN Chi-restraints excluded: chain U residue 518 LYS Chi-restraints excluded: chain U residue 545 LEU Chi-restraints excluded: chain U residue 565 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 0.0370 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.0040 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.0030 chunk 15 optimal weight: 0.9980 overall best weight: 0.3680 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.158360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.131240 restraints weight = 3175.122| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.23 r_work: 0.3503 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2216 Z= 0.117 Angle : 0.566 6.127 2986 Z= 0.301 Chirality : 0.043 0.252 328 Planarity : 0.003 0.029 395 Dihedral : 4.879 35.453 295 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.46 % Favored : 92.78 % Rotamer: Outliers : 4.96 % Allowed : 30.58 % Favored : 64.46 % 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: 0.38 (0.53), residues: 263 helix: 1.79 (0.47), residues: 127 sheet: -0.30 (0.89), residues: 21 loop : -1.47 (0.59), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 565 TYR 0.012 0.001 TYR A1176 PHE 0.010 0.001 PHE A1247 TRP 0.008 0.001 TRP A1192 HIS 0.001 0.000 HIS U 585 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 2216) covalent geometry : angle 0.56607 ( 2986) hydrogen bonds : bond 0.02932 ( 105) hydrogen bonds : angle 4.02997 ( 312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1316.87 seconds wall clock time: 23 minutes 20.50 seconds (1400.50 seconds total)