Starting phenix.real_space_refine on Sat Apr 26 16:04:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ei2_48074/04_2025/9ei2_48074.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ei2_48074/04_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_48074/04_2025/9ei2_48074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ei2_48074/04_2025/9ei2_48074.map" model { file = "/net/cci-nas-00/data/ceres_data/9ei2_48074/04_2025/9ei2_48074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ei2_48074/04_2025/9ei2_48074.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 2.76, per 1000 atoms: 1.26 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: 0.57 Conformation dependent library (CDL) restraints added in 273.7 milliseconds 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: 0.21 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: 0.53 Time building geometry restraints manager: 0.70 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: 1.370 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 12.120 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.710 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP A1192 HIS 0.002 0.001 HIS U 552 PHE 0.011 0.002 PHE A1247 TYR 0.009 0.002 TYR U 508 ARG 0.008 0.001 ARG U 577 Details of bonding type rmsd hydrogen bonds : bond 0.10374 ( 105) hydrogen bonds : angle 5.05804 ( 312) covalent geometry : bond 0.00361 ( 2216) covalent geometry : angle 0.57652 ( 2986) *********************** 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 : 0.254 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 12 residues processed: 71 average time/residue: 1.1339 time to fit residues: 82.1939 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 : 0.249 ------------------------------------------------------------------------------- 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 21 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.154301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.127767 restraints weight = 3144.624| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.20 r_work: 0.3497 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.0726 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= 0.142 Angle : 0.546 6.116 2986 Z= 0.289 Chirality : 0.042 0.150 328 Planarity : 0.004 0.028 395 Dihedral : 7.761 57.793 320 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.60 % Favored : 91.63 % Rotamer: Outliers : 8.68 % Allowed : 26.03 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.54), residues: 263 helix: 2.00 (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 TRP 0.010 0.001 TRP A1192 HIS 0.002 0.001 HIS U 552 PHE 0.011 0.002 PHE A1247 TYR 0.011 0.002 TYR A1176 ARG 0.004 0.001 ARG U 577 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 105) hydrogen bonds : angle 4.22002 ( 312) covalent geometry : bond 0.00338 ( 2216) covalent geometry : angle 0.54631 ( 2986) *********************** 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 : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1167 ARG cc_start: 0.8581 (ttm-80) cc_final: 0.8350 (ttt90) REVERT: A 1270 GLN cc_start: 0.5834 (OUTLIER) cc_final: 0.5543 (tm-30) REVERT: A 1296 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7999 (tpp) outliers start: 21 outliers final: 10 residues processed: 77 average time/residue: 1.3243 time to fit residues: 103.8579 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 : 0.246 ------------------------------------------------------------------------------- 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 4 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.0870 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.153597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.125874 restraints weight = 3105.849| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.24 r_work: 0.3495 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.0804 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= 0.138 Angle : 0.544 5.887 2986 Z= 0.289 Chirality : 0.042 0.168 328 Planarity : 0.004 0.029 395 Dihedral : 5.315 33.767 297 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.60 % Favored : 91.63 % Rotamer: Outliers : 5.79 % Allowed : 28.10 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.54), residues: 263 helix: 1.96 (0.48), residues: 129 sheet: -0.90 (0.71), residues: 28 loop : -2.02 (0.60), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1192 HIS 0.002 0.001 HIS U 552 PHE 0.011 0.002 PHE A1247 TYR 0.010 0.001 TYR A1197 ARG 0.003 0.000 ARG U 540 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 105) hydrogen bonds : angle 4.08113 ( 312) covalent geometry : bond 0.00329 ( 2216) covalent geometry : angle 0.54443 ( 2986) *********************** 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 81 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1167 ARG cc_start: 0.8598 (ttm-80) cc_final: 0.8226 (ttt-90) REVERT: A 1270 GLN cc_start: 0.5803 (OUTLIER) cc_final: 0.5526 (tm-30) REVERT: A 1296 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7961 (tpp) outliers start: 14 outliers final: 9 residues processed: 72 average time/residue: 1.2514 time to fit residues: 91.8622 Evaluate side-chains 77 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.156949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.129224 restraints weight = 3044.432| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.23 r_work: 0.3483 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.0981 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= 0.156 Angle : 0.539 5.889 2986 Z= 0.286 Chirality : 0.042 0.169 328 Planarity : 0.004 0.031 395 Dihedral : 5.314 33.729 297 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.60 % Favored : 91.63 % Rotamer: Outliers : 5.79 % Allowed : 28.93 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.53), residues: 263 helix: 1.80 (0.47), residues: 131 sheet: -0.86 (0.72), residues: 28 loop : -1.98 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1192 HIS 0.002 0.001 HIS U 552 PHE 0.012 0.002 PHE A1247 TYR 0.013 0.002 TYR A1176 ARG 0.003 0.000 ARG A1218 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 105) hydrogen bonds : angle 4.05409 ( 312) covalent geometry : bond 0.00370 ( 2216) covalent geometry : angle 0.53930 ( 2986) *********************** 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 80 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1167 ARG cc_start: 0.8593 (ttm-80) cc_final: 0.8230 (ttt-90) REVERT: A 1182 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.6958 (mm-40) REVERT: A 1270 GLN cc_start: 0.5831 (OUTLIER) cc_final: 0.5531 (tm-30) REVERT: A 1296 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7961 (tpp) outliers start: 14 outliers final: 6 residues processed: 72 average time/residue: 1.2923 time to fit residues: 94.8447 Evaluate side-chains 75 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 18 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.155936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.128545 restraints weight = 3042.258| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.18 r_work: 0.3468 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2216 Z= 0.199 Angle : 0.580 5.810 2986 Z= 0.305 Chirality : 0.043 0.154 328 Planarity : 0.004 0.033 395 Dihedral : 5.105 33.084 295 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.60 % Favored : 91.63 % Rotamer: Outliers : 4.55 % Allowed : 30.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.53), residues: 263 helix: 1.72 (0.47), residues: 131 sheet: -0.93 (0.73), residues: 28 loop : -2.01 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1192 HIS 0.002 0.001 HIS U 552 PHE 0.011 0.002 PHE A1247 TYR 0.010 0.002 TYR A1197 ARG 0.004 0.001 ARG A1218 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 105) hydrogen bonds : angle 4.17697 ( 312) covalent geometry : bond 0.00471 ( 2216) covalent geometry : angle 0.58015 ( 2986) *********************** 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 78 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1167 ARG cc_start: 0.8600 (ttm-80) cc_final: 0.8370 (ttt90) REVERT: A 1182 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.6991 (mm-40) REVERT: A 1270 GLN cc_start: 0.5862 (OUTLIER) cc_final: 0.5569 (tm-30) REVERT: A 1296 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7961 (tpp) REVERT: U 566 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7428 (mm-40) outliers start: 11 outliers final: 5 residues processed: 72 average time/residue: 1.4160 time to fit residues: 103.8656 Evaluate side-chains 74 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1182 GLN Chi-restraints excluded: chain A residue 1221 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 11 optimal weight: 0.0570 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 5 optimal weight: 0.0970 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.157754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130881 restraints weight = 3084.924| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.19 r_work: 0.3494 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1196 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= 0.114 Angle : 0.521 5.845 2986 Z= 0.276 Chirality : 0.041 0.139 328 Planarity : 0.004 0.030 395 Dihedral : 4.995 34.480 295 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.22 % Favored : 92.02 % Rotamer: Outliers : 5.37 % Allowed : 30.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.53), residues: 263 helix: 1.80 (0.47), residues: 131 sheet: -0.89 (0.72), residues: 28 loop : -1.85 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1192 HIS 0.002 0.001 HIS U 585 PHE 0.011 0.001 PHE A1247 TYR 0.016 0.002 TYR A1176 ARG 0.002 0.000 ARG U 540 Details of bonding type rmsd hydrogen bonds : bond 0.03081 ( 105) hydrogen bonds : angle 4.00341 ( 312) covalent geometry : bond 0.00272 ( 2216) covalent geometry : angle 0.52121 ( 2986) *********************** 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 77 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1167 ARG cc_start: 0.8597 (ttm-80) cc_final: 0.8235 (ttt-90) REVERT: A 1270 GLN cc_start: 0.5836 (OUTLIER) cc_final: 0.5537 (tm-30) REVERT: A 1296 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7911 (tpp) REVERT: A 1297 THR cc_start: 0.7997 (t) cc_final: 0.7795 (t) outliers start: 13 outliers final: 9 residues processed: 69 average time/residue: 1.4213 time to fit residues: 99.9182 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 : 0.268 ------------------------------------------------------------------------------- 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 1262 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 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 22 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 15 optimal weight: 0.8980 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 = 0.4000 r_free = 0.4000 target = 0.155586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.128463 restraints weight = 3095.216| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.19 r_work: 0.3493 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1186 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= 0.131 Angle : 0.542 5.816 2986 Z= 0.287 Chirality : 0.041 0.144 328 Planarity : 0.003 0.029 395 Dihedral : 4.969 34.501 295 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.22 % Favored : 92.02 % Rotamer: Outliers : 4.13 % Allowed : 31.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.53), residues: 263 helix: 1.74 (0.47), residues: 131 sheet: -0.68 (0.75), residues: 28 loop : -1.87 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1192 HIS 0.002 0.001 HIS U 585 PHE 0.011 0.001 PHE A1247 TYR 0.008 0.001 TYR A1197 ARG 0.002 0.000 ARG A1218 Details of bonding type rmsd hydrogen bonds : bond 0.03098 ( 105) hydrogen bonds : angle 4.03555 ( 312) covalent geometry : bond 0.00316 ( 2216) covalent geometry : angle 0.54213 ( 2986) *********************** 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 75 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1167 ARG cc_start: 0.8594 (ttm-80) cc_final: 0.8360 (ttt90) REVERT: A 1296 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7974 (tpp) REVERT: U 514 LEU cc_start: 0.8327 (mt) cc_final: 0.8101 (mp) outliers start: 10 outliers final: 6 residues processed: 70 average time/residue: 1.2954 time to fit residues: 92.4382 Evaluate side-chains 71 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1188 GLU Chi-restraints excluded: chain A residue 1221 MET 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 20 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.154490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.126617 restraints weight = 3155.577| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.24 r_work: 0.3487 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1312 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= 0.130 Angle : 0.568 5.853 2986 Z= 0.302 Chirality : 0.043 0.243 328 Planarity : 0.004 0.029 395 Dihedral : 4.917 34.656 295 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.60 % Favored : 91.63 % Rotamer: Outliers : 4.13 % Allowed : 32.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.53), residues: 263 helix: 1.71 (0.47), residues: 131 sheet: -0.66 (0.75), residues: 28 loop : -1.86 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1192 HIS 0.002 0.001 HIS U 585 PHE 0.011 0.001 PHE A1247 TYR 0.016 0.002 TYR A1176 ARG 0.002 0.000 ARG A1218 Details of bonding type rmsd hydrogen bonds : bond 0.03056 ( 105) hydrogen bonds : angle 4.03677 ( 312) covalent geometry : bond 0.00313 ( 2216) covalent geometry : angle 0.56775 ( 2986) *********************** 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 71 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1167 ARG cc_start: 0.8607 (ttm-80) cc_final: 0.8376 (ttt90) REVERT: A 1270 GLN cc_start: 0.5845 (OUTLIER) cc_final: 0.5541 (tm-30) REVERT: A 1296 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7924 (tpp) outliers start: 10 outliers final: 7 residues processed: 67 average time/residue: 1.2777 time to fit residues: 87.2835 Evaluate side-chains 70 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 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 2 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 10 optimal weight: 0.0970 chunk 1 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.154592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.126821 restraints weight = 3110.604| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.22 r_work: 0.3492 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1303 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= 0.130 Angle : 0.566 5.849 2986 Z= 0.301 Chirality : 0.043 0.232 328 Planarity : 0.003 0.029 395 Dihedral : 4.914 34.883 295 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.22 % Favored : 92.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.53), residues: 263 helix: 1.67 (0.47), residues: 131 sheet: -0.64 (0.76), residues: 28 loop : -1.88 (0.61), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 504 HIS 0.002 0.001 HIS U 585 PHE 0.010 0.001 PHE A1247 TYR 0.014 0.002 TYR A1176 ARG 0.002 0.000 ARG A1218 Details of bonding type rmsd hydrogen bonds : bond 0.03058 ( 105) hydrogen bonds : angle 4.04067 ( 312) covalent geometry : bond 0.00312 ( 2216) covalent geometry : angle 0.56583 ( 2986) *********************** 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: 12 poor density : 63 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1167 ARG cc_start: 0.8598 (ttm-80) cc_final: 0.8366 (ttt90) REVERT: A 1182 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.6890 (mm-40) REVERT: A 1270 GLN cc_start: 0.5854 (OUTLIER) cc_final: 0.5558 (tm-30) REVERT: A 1296 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7905 (tpp) outliers start: 12 outliers final: 8 residues processed: 68 average time/residue: 1.2935 time to fit residues: 89.6826 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 : 0.233 ------------------------------------------------------------------------------- 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 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.153725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.125833 restraints weight = 3044.249| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.22 r_work: 0.3492 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1346 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= 0.128 Angle : 0.562 5.861 2986 Z= 0.300 Chirality : 0.041 0.135 328 Planarity : 0.003 0.029 395 Dihedral : 4.908 35.034 295 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.60 % Favored : 91.63 % Rotamer: Outliers : 4.55 % Allowed : 31.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.53), residues: 263 helix: 1.62 (0.47), residues: 131 sheet: -0.22 (0.88), residues: 21 loop : -1.79 (0.59), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1192 HIS 0.002 0.000 HIS U 585 PHE 0.010 0.001 PHE A1247 TYR 0.007 0.001 TYR A1197 ARG 0.002 0.000 ARG A1218 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 105) hydrogen bonds : angle 4.05229 ( 312) covalent geometry : bond 0.00306 ( 2216) covalent geometry : angle 0.56237 ( 2986) ********************** 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 74 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1167 ARG cc_start: 0.8599 (ttm-80) cc_final: 0.8366 (ttt90) REVERT: A 1182 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6864 (mm-40) REVERT: A 1270 GLN cc_start: 0.5825 (OUTLIER) cc_final: 0.5526 (tm-30) REVERT: A 1296 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7963 (tpp) outliers start: 11 outliers final: 7 residues processed: 68 average time/residue: 1.2680 time to fit residues: 87.8743 Evaluate side-chains 73 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 545 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.157831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.130547 restraints weight = 3106.013| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.18 r_work: 0.3490 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2216 Z= 0.143 Angle : 0.581 5.858 2986 Z= 0.310 Chirality : 0.044 0.247 328 Planarity : 0.004 0.028 395 Dihedral : 4.910 34.841 295 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.84 % Favored : 92.40 % Rotamer: Outliers : 4.55 % Allowed : 31.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.53), residues: 263 helix: 1.59 (0.47), residues: 131 sheet: -0.21 (0.88), residues: 21 loop : -1.83 (0.59), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1192 HIS 0.002 0.001 HIS U 585 PHE 0.010 0.001 PHE A1247 TYR 0.015 0.002 TYR A1176 ARG 0.002 0.000 ARG A1260 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 105) hydrogen bonds : angle 4.11830 ( 312) covalent geometry : bond 0.00344 ( 2216) covalent geometry : angle 0.58140 ( 2986) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2887.73 seconds wall clock time: 49 minutes 57.95 seconds (2997.95 seconds total)