Starting phenix.real_space_refine on Wed Mar 4 16:41:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tt0_26106/03_2026/7tt0_26106.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tt0_26106/03_2026/7tt0_26106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tt0_26106/03_2026/7tt0_26106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tt0_26106/03_2026/7tt0_26106.map" model { file = "/net/cci-nas-00/data/ceres_data/7tt0_26106/03_2026/7tt0_26106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tt0_26106/03_2026/7tt0_26106.cif" } resolution = 4.3 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= 0.006 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 4820 2.51 5 N 1297 2.21 5 O 1488 1.98 5 H 7253 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14884 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 9052 Classifications: {'peptide': 588} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 565} Chain breaks: 5 Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1381 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "D" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3390 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "C" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 675 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 6, 'TRANS': 41} Chain: "P" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 386 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain breaks: 1 Time building chain proxies: 2.33, per 1000 atoms: 0.16 Number of scatterers: 14884 At special positions: 0 Unit cell: (107.382, 127.785, 104.161, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 O 1488 8.00 N 1297 7.00 C 4820 6.00 H 7253 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS P1299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 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: 1.16 Conformation dependent library (CDL) restraints added in 422.6 milliseconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1762 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 7 sheets defined 33.5% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 189 through 197 removed outlier: 4.594A pdb=" N ILE A 194 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N SER A 195 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 232 Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.742A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 366 removed outlier: 3.886A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.937A pdb=" N GLY A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'E' and resid 23 through 27 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.504A pdb=" N ALA D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 120 removed outlier: 3.671A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.061A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.599A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 215 " --> pdb=" O THR D 211 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 242 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 76 through 80 Processing sheet with id=AA1, first strand: chain 'A' and resid 239 through 242 removed outlier: 6.929A pdb=" N ASN A 259 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 276 removed outlier: 5.878A pdb=" N VAL A 335 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY A 270 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 355 removed outlier: 5.892A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ARG A 350 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 12.886A pdb=" N TYR A 416 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N ILE A 352 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 12.449A pdb=" N VAL A 418 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N PHE A 354 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 11.891A pdb=" N GLU A 420 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 802 through 806 removed outlier: 6.365A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG P1269 " --> pdb=" O VAL P1272 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N PHE P1274 " --> pdb=" O GLU P1267 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLU P1267 " --> pdb=" O PHE P1274 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.327A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 32 through 34 removed outlier: 3.955A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 32 through 34 removed outlier: 6.946A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1098 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: 3.17 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 7253 1.03 - 1.23: 177 1.23 - 1.43: 3294 1.43 - 1.63: 4290 1.63 - 1.83: 48 Bond restraints: 15062 Sorted by residual: bond pdb=" CG ARG D 173 " pdb=" CD ARG D 173 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CA LEU D 87 " pdb=" C LEU D 87 " ideal model delta sigma weight residual 1.522 1.506 0.015 1.40e-02 5.10e+03 1.22e+00 bond pdb=" CG ARG A 366 " pdb=" CD ARG A 366 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.16e+00 bond pdb=" CB TRP A 576 " pdb=" CG TRP A 576 " ideal model delta sigma weight residual 1.498 1.465 0.033 3.10e-02 1.04e+03 1.11e+00 bond pdb=" CA MET D 218 " pdb=" C MET D 218 " ideal model delta sigma weight residual 1.524 1.511 0.013 1.32e-02 5.74e+03 9.75e-01 ... (remaining 15057 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 26153 1.66 - 3.32: 769 3.32 - 4.98: 80 4.98 - 6.64: 3 6.64 - 8.30: 2 Bond angle restraints: 27007 Sorted by residual: angle pdb=" N ASP A 332 " pdb=" CA ASP A 332 " pdb=" C ASP A 332 " ideal model delta sigma weight residual 108.76 100.46 8.30 1.69e+00 3.50e-01 2.41e+01 angle pdb=" N GLY A 431 " pdb=" CA GLY A 431 " pdb=" C GLY A 431 " ideal model delta sigma weight residual 111.62 104.90 6.72 1.77e+00 3.19e-01 1.44e+01 angle pdb=" N MET D 225 " pdb=" CA MET D 225 " pdb=" C MET D 225 " ideal model delta sigma weight residual 109.76 103.65 6.11 1.64e+00 3.72e-01 1.39e+01 angle pdb=" N VAL A 382 " pdb=" CA VAL A 382 " pdb=" C VAL A 382 " ideal model delta sigma weight residual 111.58 108.21 3.37 1.06e+00 8.90e-01 1.01e+01 angle pdb=" N GLN D 224 " pdb=" CA GLN D 224 " pdb=" C GLN D 224 " ideal model delta sigma weight residual 111.82 108.26 3.56 1.16e+00 7.43e-01 9.41e+00 ... (remaining 27002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 6805 17.27 - 34.54: 217 34.54 - 51.80: 116 51.80 - 69.07: 45 69.07 - 86.34: 8 Dihedral angle restraints: 7191 sinusoidal: 3829 harmonic: 3362 Sorted by residual: dihedral pdb=" CB GLU A 283 " pdb=" CG GLU A 283 " pdb=" CD GLU A 283 " pdb=" OE1 GLU A 283 " ideal model delta sinusoidal sigma weight residual 0.00 83.98 -83.98 1 3.00e+01 1.11e-03 9.55e+00 dihedral pdb=" CA ALA C 52 " pdb=" C ALA C 52 " pdb=" N PRO C 53 " pdb=" CA PRO C 53 " ideal model delta harmonic sigma weight residual 180.00 164.65 15.35 0 5.00e+00 4.00e-02 9.42e+00 dihedral pdb=" CB GLU E 84 " pdb=" CG GLU E 84 " pdb=" CD GLU E 84 " pdb=" OE1 GLU E 84 " ideal model delta sinusoidal sigma weight residual 0.00 -81.29 81.29 1 3.00e+01 1.11e-03 9.05e+00 ... (remaining 7188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 756 0.040 - 0.079: 248 0.079 - 0.119: 82 0.119 - 0.158: 27 0.158 - 0.198: 2 Chirality restraints: 1115 Sorted by residual: chirality pdb=" CA TYR A 585 " pdb=" N TYR A 585 " pdb=" C TYR A 585 " pdb=" CB TYR A 585 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" CA ILE A 806 " pdb=" N ILE A 806 " pdb=" C ILE A 806 " pdb=" CB ILE A 806 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA ARG A 366 " pdb=" N ARG A 366 " pdb=" C ARG A 366 " pdb=" CB ARG A 366 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 1112 not shown) Planarity restraints: 2310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 86 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C PRO D 86 " -0.061 2.00e-02 2.50e+03 pdb=" O PRO D 86 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU D 87 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 325 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.78e+00 pdb=" C MET A 325 " -0.045 2.00e-02 2.50e+03 pdb=" O MET A 325 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO A 326 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 33 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C ASN D 33 " -0.041 2.00e-02 2.50e+03 pdb=" O ASN D 33 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU D 34 " 0.014 2.00e-02 2.50e+03 ... (remaining 2307 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 505 2.16 - 2.77: 28627 2.77 - 3.38: 38432 3.38 - 3.99: 50343 3.99 - 4.60: 78570 Nonbonded interactions: 196477 Sorted by model distance: nonbonded pdb=" OE1 GLN A 445 " pdb=" HZ2 LYS A 808 " model vdw 1.552 2.450 nonbonded pdb=" OD1 ASP E 31 " pdb=" H GLY E 82 " model vdw 1.555 2.450 nonbonded pdb=" HG SER A 715 " pdb=" OD1 ASP A 740 " model vdw 1.566 2.450 nonbonded pdb=" HD1 HIS A 533 " pdb=" OD1 ASP A 568 " model vdw 1.569 2.450 nonbonded pdb="HE22 GLN E 34 " pdb=" O GLY D 189 " model vdw 1.588 2.450 ... (remaining 196472 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 0.080 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.140 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 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 : 0.005 0.034 7811 Z= 0.226 Angle : 0.837 8.296 10599 Z= 0.527 Chirality : 0.046 0.198 1115 Planarity : 0.005 0.035 1402 Dihedral : 10.421 86.340 2832 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.26), residues: 940 helix: 0.80 (0.28), residues: 273 sheet: 1.04 (0.30), residues: 276 loop : 1.01 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.003 ARG A 661 TYR 0.024 0.003 TYR A 468 PHE 0.031 0.002 PHE A 586 TRP 0.018 0.003 TRP A 546 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 7809) covalent geometry : angle 0.83596 (10595) SS BOND : bond 0.00137 ( 2) SS BOND : angle 2.40048 ( 4) hydrogen bonds : bond 0.13069 ( 397) hydrogen bonds : angle 6.44288 ( 1098) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.8933 (m-80) cc_final: 0.8587 (m-80) REVERT: A 322 VAL cc_start: 0.8610 (t) cc_final: 0.8069 (p) REVERT: A 401 ASP cc_start: 0.8220 (t0) cc_final: 0.8000 (t0) REVERT: A 449 TRP cc_start: 0.8276 (t60) cc_final: 0.8029 (t60) REVERT: A 450 LEU cc_start: 0.9073 (mt) cc_final: 0.8818 (mt) REVERT: A 701 LYS cc_start: 0.8881 (tttt) cc_final: 0.8676 (ttmm) REVERT: A 731 ASN cc_start: 0.9218 (m-40) cc_final: 0.8948 (t0) REVERT: E 26 VAL cc_start: 0.9440 (m) cc_final: 0.9219 (p) REVERT: E 91 LEU cc_start: 0.9170 (tp) cc_final: 0.8872 (tp) REVERT: D 127 PHE cc_start: 0.8758 (t80) cc_final: 0.8290 (t80) REVERT: D 227 MET cc_start: 0.8430 (mtt) cc_final: 0.8060 (mtt) REVERT: D 234 VAL cc_start: 0.9166 (t) cc_final: 0.8881 (p) REVERT: C 81 ASP cc_start: 0.8210 (t0) cc_final: 0.7947 (t0) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.2116 time to fit residues: 85.1423 Evaluate side-chains 195 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 GLN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.146615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107279 restraints weight = 48750.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.110458 restraints weight = 25972.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111628 restraints weight = 18595.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.111984 restraints weight = 14076.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112535 restraints weight = 13440.966| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7811 Z= 0.129 Angle : 0.531 4.100 10599 Z= 0.300 Chirality : 0.043 0.157 1115 Planarity : 0.005 0.045 1402 Dihedral : 5.032 79.011 1066 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.27), residues: 940 helix: 2.22 (0.31), residues: 274 sheet: 0.64 (0.30), residues: 281 loop : 0.92 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 223 TYR 0.020 0.001 TYR C 41 PHE 0.016 0.001 PHE A 586 TRP 0.010 0.001 TRP A 739 HIS 0.004 0.001 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7809) covalent geometry : angle 0.53051 (10595) SS BOND : bond 0.00144 ( 2) SS BOND : angle 0.80687 ( 4) hydrogen bonds : bond 0.04779 ( 397) hydrogen bonds : angle 5.45568 ( 1098) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 TYR cc_start: 0.8699 (m-80) cc_final: 0.8336 (m-80) REVERT: A 401 ASP cc_start: 0.8340 (t0) cc_final: 0.8000 (t0) REVERT: A 427 ASN cc_start: 0.8548 (p0) cc_final: 0.8337 (p0) REVERT: A 449 TRP cc_start: 0.8316 (t60) cc_final: 0.7846 (t60) REVERT: A 450 LEU cc_start: 0.9067 (mt) cc_final: 0.8827 (mt) REVERT: A 701 LYS cc_start: 0.8873 (tttt) cc_final: 0.8482 (ttmm) REVERT: E 26 VAL cc_start: 0.9506 (m) cc_final: 0.9297 (p) REVERT: E 66 ASP cc_start: 0.8338 (t0) cc_final: 0.8055 (t0) REVERT: E 103 ASN cc_start: 0.8079 (t0) cc_final: 0.7327 (m110) REVERT: D 82 ASN cc_start: 0.8481 (t0) cc_final: 0.8246 (t0) REVERT: D 109 MET cc_start: 0.8712 (mtt) cc_final: 0.8452 (mmt) REVERT: D 127 PHE cc_start: 0.8682 (t80) cc_final: 0.8243 (t80) REVERT: D 154 TYR cc_start: 0.8005 (m-80) cc_final: 0.7652 (m-80) REVERT: D 227 MET cc_start: 0.7924 (mtt) cc_final: 0.7714 (mmm) REVERT: D 234 VAL cc_start: 0.9128 (t) cc_final: 0.8848 (p) REVERT: C 80 LEU cc_start: 0.8553 (mt) cc_final: 0.8346 (mt) REVERT: C 81 ASP cc_start: 0.7812 (t0) cc_final: 0.7540 (t0) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1639 time to fit residues: 53.6056 Evaluate side-chains 177 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 85 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 59 optimal weight: 0.3980 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 ASN A 542 GLN A 651 ASN A 805 ASN D 241 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.146220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.106749 restraints weight = 48833.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.109193 restraints weight = 26307.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.110791 restraints weight = 19284.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111080 restraints weight = 15224.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111588 restraints weight = 14256.873| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7811 Z= 0.125 Angle : 0.489 4.475 10599 Z= 0.273 Chirality : 0.042 0.148 1115 Planarity : 0.005 0.085 1402 Dihedral : 4.926 79.490 1066 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.12 % Allowed : 0.37 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.27), residues: 940 helix: 2.23 (0.31), residues: 276 sheet: 0.51 (0.30), residues: 281 loop : 0.83 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 97 TYR 0.013 0.001 TYR D 184 PHE 0.016 0.001 PHE D 147 TRP 0.008 0.001 TRP A 739 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7809) covalent geometry : angle 0.48694 (10595) SS BOND : bond 0.02094 ( 2) SS BOND : angle 2.50157 ( 4) hydrogen bonds : bond 0.04222 ( 397) hydrogen bonds : angle 5.20288 ( 1098) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 TYR cc_start: 0.8676 (t80) cc_final: 0.7646 (t80) REVERT: A 401 ASP cc_start: 0.8308 (t0) cc_final: 0.7928 (t0) REVERT: A 449 TRP cc_start: 0.8251 (t60) cc_final: 0.7855 (t60) REVERT: A 450 LEU cc_start: 0.9071 (mt) cc_final: 0.8829 (mt) REVERT: A 701 LYS cc_start: 0.8860 (tttt) cc_final: 0.8472 (ttmm) REVERT: A 731 ASN cc_start: 0.9291 (t0) cc_final: 0.9069 (t0) REVERT: A 774 LEU cc_start: 0.8642 (tp) cc_final: 0.8431 (tp) REVERT: E 26 VAL cc_start: 0.9514 (m) cc_final: 0.9292 (p) REVERT: E 94 THR cc_start: 0.9128 (p) cc_final: 0.8782 (p) REVERT: E 103 ASN cc_start: 0.8394 (t0) cc_final: 0.7586 (m110) REVERT: D 50 GLN cc_start: 0.8855 (mt0) cc_final: 0.8530 (mt0) REVERT: D 82 ASN cc_start: 0.8534 (t0) cc_final: 0.8268 (t0) REVERT: D 127 PHE cc_start: 0.8653 (t80) cc_final: 0.8254 (t80) REVERT: D 154 TYR cc_start: 0.7893 (m-80) cc_final: 0.7579 (m-80) REVERT: D 227 MET cc_start: 0.8081 (mtt) cc_final: 0.7850 (mmm) outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.1632 time to fit residues: 50.1478 Evaluate side-chains 174 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.0370 chunk 15 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 19 optimal weight: 0.2980 chunk 45 optimal weight: 4.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.149394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.106960 restraints weight = 45112.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.112033 restraints weight = 19880.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.115275 restraints weight = 12454.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117162 restraints weight = 9558.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.118243 restraints weight = 8247.228| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7811 Z= 0.100 Angle : 0.464 4.459 10599 Z= 0.257 Chirality : 0.041 0.147 1115 Planarity : 0.004 0.044 1402 Dihedral : 4.830 80.979 1066 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.27), residues: 940 helix: 2.25 (0.31), residues: 278 sheet: 0.53 (0.30), residues: 279 loop : 0.77 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 404 TYR 0.012 0.001 TYR D 184 PHE 0.014 0.001 PHE A 648 TRP 0.007 0.001 TRP A 576 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 7809) covalent geometry : angle 0.46193 (10595) SS BOND : bond 0.00902 ( 2) SS BOND : angle 2.43877 ( 4) hydrogen bonds : bond 0.03810 ( 397) hydrogen bonds : angle 4.91074 ( 1098) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8190 (m-80) cc_final: 0.7751 (m-10) REVERT: A 449 TRP cc_start: 0.8093 (t60) cc_final: 0.7746 (t60) REVERT: A 450 LEU cc_start: 0.9099 (mt) cc_final: 0.8866 (mt) REVERT: A 701 LYS cc_start: 0.8843 (tttt) cc_final: 0.8467 (ttmm) REVERT: A 731 ASN cc_start: 0.9175 (t0) cc_final: 0.8901 (t0) REVERT: E 66 ASP cc_start: 0.8423 (t0) cc_final: 0.8057 (t70) REVERT: D 50 GLN cc_start: 0.8820 (mt0) cc_final: 0.8504 (mt0) REVERT: D 82 ASN cc_start: 0.8516 (t0) cc_final: 0.8260 (t0) REVERT: D 127 PHE cc_start: 0.8531 (t80) cc_final: 0.8213 (t80) REVERT: D 219 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8356 (tm-30) REVERT: D 227 MET cc_start: 0.7971 (mtt) cc_final: 0.7731 (mmm) REVERT: C 81 ASP cc_start: 0.8109 (t70) cc_final: 0.7733 (t0) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1595 time to fit residues: 48.5157 Evaluate side-chains 174 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 76 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN A 805 ASN D 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.145501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.103127 restraints weight = 45879.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.107714 restraints weight = 22047.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.110529 restraints weight = 14455.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.112303 restraints weight = 11423.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.113121 restraints weight = 9960.679| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7811 Z= 0.136 Angle : 0.477 3.583 10599 Z= 0.266 Chirality : 0.041 0.146 1115 Planarity : 0.004 0.046 1402 Dihedral : 4.815 84.461 1066 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.12 % Allowed : 0.62 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.27), residues: 940 helix: 2.22 (0.30), residues: 278 sheet: 0.30 (0.30), residues: 279 loop : 0.60 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 404 TYR 0.026 0.001 TYR E 75 PHE 0.015 0.001 PHE A 648 TRP 0.007 0.001 TRP A 576 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7809) covalent geometry : angle 0.47580 (10595) SS BOND : bond 0.00056 ( 2) SS BOND : angle 1.93653 ( 4) hydrogen bonds : bond 0.03737 ( 397) hydrogen bonds : angle 4.93800 ( 1098) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8262 (m-80) cc_final: 0.7810 (m-10) REVERT: A 449 TRP cc_start: 0.8240 (t60) cc_final: 0.7877 (t60) REVERT: A 450 LEU cc_start: 0.9101 (mt) cc_final: 0.8888 (mt) REVERT: A 508 SER cc_start: 0.7622 (p) cc_final: 0.7310 (m) REVERT: A 701 LYS cc_start: 0.8804 (tttt) cc_final: 0.8409 (ttmm) REVERT: A 731 ASN cc_start: 0.9166 (t0) cc_final: 0.8927 (t0) REVERT: E 26 VAL cc_start: 0.9396 (t) cc_final: 0.9158 (p) REVERT: D 50 GLN cc_start: 0.8861 (mt0) cc_final: 0.8540 (mt0) REVERT: D 82 ASN cc_start: 0.8444 (t0) cc_final: 0.8178 (t0) REVERT: D 127 PHE cc_start: 0.8527 (t80) cc_final: 0.8229 (t80) REVERT: D 227 MET cc_start: 0.7707 (mtt) cc_final: 0.7416 (mmm) outliers start: 1 outliers final: 0 residues processed: 195 average time/residue: 0.1520 time to fit residues: 42.0268 Evaluate side-chains 169 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 84 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 ASN D 116 ASN D 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.145752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.102193 restraints weight = 45170.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106992 restraints weight = 20637.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.110039 restraints weight = 13279.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111780 restraints weight = 10352.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112855 restraints weight = 9055.323| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7811 Z= 0.123 Angle : 0.467 4.073 10599 Z= 0.258 Chirality : 0.041 0.154 1115 Planarity : 0.005 0.111 1402 Dihedral : 4.837 84.899 1066 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.12 % Allowed : 0.37 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.27), residues: 940 helix: 2.11 (0.30), residues: 278 sheet: 0.19 (0.30), residues: 279 loop : 0.56 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 97 TYR 0.013 0.001 TYR D 184 PHE 0.020 0.001 PHE A 804 TRP 0.008 0.001 TRP A 576 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7809) covalent geometry : angle 0.46483 (10595) SS BOND : bond 0.00114 ( 2) SS BOND : angle 2.20445 ( 4) hydrogen bonds : bond 0.03678 ( 397) hydrogen bonds : angle 4.84471 ( 1098) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8359 (m-80) cc_final: 0.7883 (m-10) REVERT: A 449 TRP cc_start: 0.8157 (t60) cc_final: 0.7812 (t60) REVERT: A 450 LEU cc_start: 0.9068 (mt) cc_final: 0.8857 (mt) REVERT: A 508 SER cc_start: 0.7753 (p) cc_final: 0.7388 (m) REVERT: A 701 LYS cc_start: 0.8832 (tttt) cc_final: 0.8464 (ttmm) REVERT: A 731 ASN cc_start: 0.9208 (t0) cc_final: 0.8960 (t0) REVERT: E 26 VAL cc_start: 0.9422 (t) cc_final: 0.9191 (p) REVERT: E 66 ASP cc_start: 0.8522 (t0) cc_final: 0.8171 (t70) REVERT: E 75 TYR cc_start: 0.8010 (m-80) cc_final: 0.7291 (m-80) REVERT: D 50 GLN cc_start: 0.8863 (mt0) cc_final: 0.8552 (mt0) REVERT: D 82 ASN cc_start: 0.8511 (t0) cc_final: 0.8246 (t0) REVERT: D 127 PHE cc_start: 0.8615 (t80) cc_final: 0.8312 (t80) REVERT: D 227 MET cc_start: 0.7912 (mtt) cc_final: 0.7667 (mmm) REVERT: C 82 ILE cc_start: 0.7517 (pt) cc_final: 0.7281 (tt) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.1533 time to fit residues: 42.1507 Evaluate side-chains 167 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 21 optimal weight: 0.7980 chunk 58 optimal weight: 0.0670 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN A 805 ASN D 116 ASN D 226 GLN D 241 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.144147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.104669 restraints weight = 48648.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105860 restraints weight = 28321.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.107628 restraints weight = 23176.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.107978 restraints weight = 17105.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108967 restraints weight = 15561.629| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 7811 Z= 0.124 Angle : 0.478 7.088 10599 Z= 0.264 Chirality : 0.043 0.403 1115 Planarity : 0.004 0.051 1402 Dihedral : 4.754 82.078 1066 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.25 % Allowed : 0.87 % Favored : 98.89 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.27), residues: 940 helix: 2.21 (0.30), residues: 277 sheet: 0.13 (0.30), residues: 283 loop : 0.48 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 223 TYR 0.013 0.001 TYR A 578 PHE 0.023 0.001 PHE A 785 TRP 0.007 0.001 TRP A 576 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7809) covalent geometry : angle 0.47235 (10595) SS BOND : bond 0.01663 ( 2) SS BOND : angle 3.63636 ( 4) hydrogen bonds : bond 0.03495 ( 397) hydrogen bonds : angle 4.76787 ( 1098) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8140 (m-80) cc_final: 0.7756 (m-10) REVERT: A 449 TRP cc_start: 0.8233 (t60) cc_final: 0.7894 (t60) REVERT: A 508 SER cc_start: 0.7737 (p) cc_final: 0.7380 (m) REVERT: A 701 LYS cc_start: 0.8841 (tttt) cc_final: 0.8445 (ttmm) REVERT: A 731 ASN cc_start: 0.9323 (t0) cc_final: 0.9065 (t0) REVERT: E 26 VAL cc_start: 0.9520 (t) cc_final: 0.9314 (p) REVERT: E 66 ASP cc_start: 0.8647 (t0) cc_final: 0.8305 (t70) REVERT: E 75 TYR cc_start: 0.7894 (m-80) cc_final: 0.7375 (m-80) REVERT: D 50 GLN cc_start: 0.8907 (mt0) cc_final: 0.8599 (mt0) REVERT: D 82 ASN cc_start: 0.8483 (t0) cc_final: 0.8220 (t0) REVERT: D 127 PHE cc_start: 0.8736 (t80) cc_final: 0.8383 (t80) REVERT: D 145 SER cc_start: 0.9051 (p) cc_final: 0.8754 (t) REVERT: D 227 MET cc_start: 0.7999 (mtt) cc_final: 0.7779 (mmm) REVERT: C 82 ILE cc_start: 0.7525 (pt) cc_final: 0.7299 (tt) outliers start: 2 outliers final: 0 residues processed: 191 average time/residue: 0.1477 time to fit residues: 40.2751 Evaluate side-chains 168 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 70 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 ASN D 116 ASN D 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.145470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.102147 restraints weight = 45811.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.106914 restraints weight = 20907.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109935 restraints weight = 13456.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111654 restraints weight = 10489.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.112539 restraints weight = 9151.988| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7811 Z= 0.131 Angle : 0.472 5.279 10599 Z= 0.261 Chirality : 0.042 0.339 1115 Planarity : 0.004 0.046 1402 Dihedral : 4.716 77.838 1066 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.12 % Allowed : 0.62 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.27), residues: 940 helix: 2.23 (0.31), residues: 277 sheet: -0.00 (0.29), residues: 285 loop : 0.46 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 223 TYR 0.014 0.001 TYR D 184 PHE 0.012 0.001 PHE A 785 TRP 0.008 0.001 TRP A 576 HIS 0.002 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7809) covalent geometry : angle 0.46888 (10595) SS BOND : bond 0.01637 ( 2) SS BOND : angle 2.72763 ( 4) hydrogen bonds : bond 0.03498 ( 397) hydrogen bonds : angle 4.76212 ( 1098) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8403 (m-80) cc_final: 0.7954 (m-10) REVERT: A 449 TRP cc_start: 0.8091 (t60) cc_final: 0.7809 (t60) REVERT: A 508 SER cc_start: 0.7796 (p) cc_final: 0.7437 (m) REVERT: A 701 LYS cc_start: 0.8812 (tttt) cc_final: 0.8452 (ttmm) REVERT: A 731 ASN cc_start: 0.9247 (t0) cc_final: 0.8989 (t0) REVERT: E 41 ASN cc_start: 0.9091 (p0) cc_final: 0.8891 (p0) REVERT: E 66 ASP cc_start: 0.8697 (t0) cc_final: 0.8318 (t70) REVERT: E 75 TYR cc_start: 0.7980 (m-80) cc_final: 0.7317 (m-80) REVERT: D 82 ASN cc_start: 0.8517 (t0) cc_final: 0.8245 (t0) REVERT: D 127 PHE cc_start: 0.8636 (t80) cc_final: 0.8342 (t80) REVERT: C 82 ILE cc_start: 0.7649 (pt) cc_final: 0.7449 (tt) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.1563 time to fit residues: 43.6174 Evaluate side-chains 164 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN D 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.143230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.096821 restraints weight = 49161.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101708 restraints weight = 23822.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.104741 restraints weight = 15979.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.106390 restraints weight = 12788.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.107489 restraints weight = 11358.546| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7811 Z= 0.131 Angle : 0.499 9.362 10599 Z= 0.274 Chirality : 0.043 0.409 1115 Planarity : 0.004 0.045 1402 Dihedral : 4.683 67.076 1066 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.12 % Allowed : 0.50 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.27), residues: 940 helix: 2.26 (0.31), residues: 277 sheet: -0.08 (0.29), residues: 285 loop : 0.36 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 223 TYR 0.016 0.001 TYR A 468 PHE 0.009 0.001 PHE A 648 TRP 0.008 0.001 TRP A 576 HIS 0.002 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7809) covalent geometry : angle 0.49159 (10595) SS BOND : bond 0.03835 ( 2) SS BOND : angle 4.51607 ( 4) hydrogen bonds : bond 0.03476 ( 397) hydrogen bonds : angle 4.76449 ( 1098) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8550 (m-80) cc_final: 0.8090 (m-10) REVERT: A 449 TRP cc_start: 0.8142 (t60) cc_final: 0.7859 (t60) REVERT: A 508 SER cc_start: 0.7679 (p) cc_final: 0.7292 (m) REVERT: A 701 LYS cc_start: 0.8821 (tttt) cc_final: 0.8495 (ttmm) REVERT: A 731 ASN cc_start: 0.9220 (t0) cc_final: 0.8961 (t0) REVERT: E 41 ASN cc_start: 0.9075 (p0) cc_final: 0.8868 (p0) REVERT: E 75 TYR cc_start: 0.8016 (m-80) cc_final: 0.7326 (m-80) REVERT: D 82 ASN cc_start: 0.8483 (t0) cc_final: 0.8209 (t0) REVERT: D 127 PHE cc_start: 0.8635 (t80) cc_final: 0.8347 (t80) REVERT: P 1298 TYR cc_start: 0.8075 (t80) cc_final: 0.7858 (t80) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.1588 time to fit residues: 42.4343 Evaluate side-chains 165 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN D 116 ASN D 241 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.143270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.096838 restraints weight = 48724.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.101663 restraints weight = 23642.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.104687 restraints weight = 15837.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.106238 restraints weight = 12661.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.107404 restraints weight = 11271.451| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7811 Z= 0.120 Angle : 0.489 6.499 10599 Z= 0.268 Chirality : 0.042 0.364 1115 Planarity : 0.004 0.044 1402 Dihedral : 4.600 63.402 1066 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.27), residues: 940 helix: 2.26 (0.31), residues: 277 sheet: -0.14 (0.29), residues: 283 loop : 0.35 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 97 TYR 0.014 0.001 TYR D 184 PHE 0.010 0.001 PHE A 648 TRP 0.009 0.001 TRP A 739 HIS 0.002 0.000 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7809) covalent geometry : angle 0.48482 (10595) SS BOND : bond 0.02652 ( 2) SS BOND : angle 3.49524 ( 4) hydrogen bonds : bond 0.03425 ( 397) hydrogen bonds : angle 4.70115 ( 1098) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 PHE cc_start: 0.8578 (m-80) cc_final: 0.8118 (m-10) REVERT: A 449 TRP cc_start: 0.8112 (t60) cc_final: 0.7817 (t60) REVERT: A 508 SER cc_start: 0.7799 (p) cc_final: 0.7441 (m) REVERT: A 701 LYS cc_start: 0.8829 (tttt) cc_final: 0.8513 (ttmm) REVERT: A 731 ASN cc_start: 0.9231 (t0) cc_final: 0.8974 (t0) REVERT: E 41 ASN cc_start: 0.9085 (p0) cc_final: 0.8866 (p0) REVERT: D 82 ASN cc_start: 0.8484 (t0) cc_final: 0.8224 (t0) REVERT: D 127 PHE cc_start: 0.8645 (t80) cc_final: 0.8373 (t80) REVERT: C 83 ARG cc_start: 0.7474 (mpp80) cc_final: 0.7254 (mpp80) REVERT: P 1298 TYR cc_start: 0.8089 (t80) cc_final: 0.7888 (t80) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1551 time to fit residues: 41.2626 Evaluate side-chains 164 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 39 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 ASN D 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.143634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.105509 restraints weight = 48786.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.110806 restraints weight = 29960.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110334 restraints weight = 24206.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.111874 restraints weight = 15549.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.112678 restraints weight = 13515.368| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7811 Z= 0.112 Angle : 0.480 7.350 10599 Z= 0.263 Chirality : 0.042 0.352 1115 Planarity : 0.004 0.043 1402 Dihedral : 4.594 61.997 1066 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.12 % Allowed : 0.25 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.28), residues: 940 helix: 2.25 (0.31), residues: 278 sheet: -0.17 (0.30), residues: 285 loop : 0.36 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 223 TYR 0.014 0.001 TYR D 184 PHE 0.011 0.001 PHE D 95 TRP 0.009 0.001 TRP A 739 HIS 0.002 0.000 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 7809) covalent geometry : angle 0.47588 (10595) SS BOND : bond 0.02664 ( 2) SS BOND : angle 3.19182 ( 4) hydrogen bonds : bond 0.03347 ( 397) hydrogen bonds : angle 4.65727 ( 1098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2789.19 seconds wall clock time: 48 minutes 6.66 seconds (2886.66 seconds total)