Starting phenix.real_space_refine on Tue Aug 4 21:36:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jh8_61475/08_2026/9jh8_61475.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jh8_61475/08_2026/9jh8_61475.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jh8_61475/08_2026/9jh8_61475.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jh8_61475/08_2026/9jh8_61475.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jh8_61475/08_2026/9jh8_61475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jh8_61475/08_2026/9jh8_61475.map" } resolution = 3.81 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= 0.001 sd= 0.009 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 34 5.49 5 S 20 5.16 5 C 4244 2.51 5 N 1118 2.21 5 O 1337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6754 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6036 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain: "C" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 358 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.64, per 1000 atoms: 0.24 Number of scatterers: 6754 At special positions: 0 Unit cell: (71.34, 82.82, 105.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 20 16.00 P 34 15.00 O 1337 8.00 N 1118 7.00 C 4244 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: 0.69 Conformation dependent library (CDL) restraints added in 445.9 milliseconds 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1394 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 12 sheets defined 31.9% alpha, 16.8% beta 9 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.722A pdb=" N TYR A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 281 through 289 Processing helix chain 'A' and resid 289 through 301 removed outlier: 4.519A pdb=" N GLN A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 388 through 404 Processing helix chain 'A' and resid 439 through 453 removed outlier: 3.794A pdb=" N TYR A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 485 removed outlier: 3.570A pdb=" N LEU A 485 " --> pdb=" O ILE A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 505 through 523 removed outlier: 3.887A pdb=" N LEU A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 603 removed outlier: 3.696A pdb=" N LEU A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.825A pdb=" N TYR A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 712 Processing helix chain 'A' and resid 723 through 735 Processing helix chain 'A' and resid 736 through 739 removed outlier: 4.107A pdb=" N ILE A 739 " --> pdb=" O ILE A 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 736 through 739' Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.509A pdb=" N ASN A 9 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 651 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 126 removed outlier: 3.508A pdb=" N LEU A 134 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N VAL A 172 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 62 removed outlier: 4.049A pdb=" N LYS A 88 " --> pdb=" O GLN A 28 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LYS A 30 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N PHE A 86 " --> pdb=" O LYS A 30 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA5, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA6, first strand: chain 'A' and resid 268 through 271 removed outlier: 6.750A pdb=" N ILE A 259 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL A 219 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASN A 261 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU A 214 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.960A pdb=" N GLY A 357 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU A 352 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 378 through 379 removed outlier: 6.242A pdb=" N VAL A 378 " --> pdb=" O GLU A 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 384 through 385 removed outlier: 5.816A pdb=" N TYR A 384 " --> pdb=" O TYR A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB2, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AB3, first strand: chain 'A' and resid 559 through 560 removed outlier: 6.830A pdb=" N ILE A 637 " --> pdb=" O SER A 693 " (cutoff:3.500A) 233 hydrogen bonds defined for protein. 669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1479 1.33 - 1.45: 1644 1.45 - 1.57: 3740 1.57 - 1.69: 65 1.69 - 1.81: 35 Bond restraints: 6963 Sorted by residual: bond pdb=" C3' DG C 8 " pdb=" O3' DG C 8 " ideal model delta sigma weight residual 1.435 1.352 0.083 1.30e-02 5.92e+03 4.11e+01 bond pdb=" C3' DT C 9 " pdb=" O3' DT C 9 " ideal model delta sigma weight residual 1.435 1.353 0.082 1.30e-02 5.92e+03 4.00e+01 bond pdb=" N9 DA E 13 " pdb=" C4 DA E 13 " ideal model delta sigma weight residual 1.374 1.337 0.037 6.00e-03 2.78e+04 3.83e+01 bond pdb=" C3' DA C 7 " pdb=" O3' DA C 7 " ideal model delta sigma weight residual 1.435 1.359 0.076 1.30e-02 5.92e+03 3.46e+01 bond pdb=" N7 DA E 13 " pdb=" C5 DA E 13 " ideal model delta sigma weight residual 1.388 1.355 0.033 6.00e-03 2.78e+04 2.99e+01 ... (remaining 6958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 9365 3.50 - 7.00: 152 7.00 - 10.50: 16 10.50 - 13.99: 3 13.99 - 17.49: 1 Bond angle restraints: 9537 Sorted by residual: angle pdb=" O4' DT E 9 " pdb=" C4' DT E 9 " pdb=" C3' DT E 9 " ideal model delta sigma weight residual 106.00 102.45 3.55 6.00e-01 2.78e+00 3.49e+01 angle pdb=" O4' DT C 9 " pdb=" C4' DT C 9 " pdb=" C3' DT C 9 " ideal model delta sigma weight residual 106.00 102.74 3.26 6.00e-01 2.78e+00 2.95e+01 angle pdb=" O4' DT C 6 " pdb=" C4' DT C 6 " pdb=" C3' DT C 6 " ideal model delta sigma weight residual 106.00 102.80 3.20 6.00e-01 2.78e+00 2.85e+01 angle pdb=" O4' DG C 4 " pdb=" C1' DG C 4 " pdb=" N9 DG C 4 " ideal model delta sigma weight residual 108.00 111.57 -3.57 7.00e-01 2.04e+00 2.61e+01 angle pdb=" O4' DA E 6 " pdb=" C4' DA E 6 " pdb=" C3' DA E 6 " ideal model delta sigma weight residual 106.00 102.99 3.01 6.00e-01 2.78e+00 2.51e+01 ... (remaining 9532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.51: 3779 23.51 - 47.02: 259 47.02 - 70.54: 79 70.54 - 94.05: 11 94.05 - 117.56: 1 Dihedral angle restraints: 4129 sinusoidal: 1942 harmonic: 2187 Sorted by residual: dihedral pdb=" CA GLU A 470 " pdb=" C GLU A 470 " pdb=" N ILE A 471 " pdb=" CA ILE A 471 " ideal model delta harmonic sigma weight residual -180.00 -147.48 -32.52 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA ILE A 471 " pdb=" C ILE A 471 " pdb=" N GLU A 472 " pdb=" CA GLU A 472 " ideal model delta harmonic sigma weight residual 180.00 -149.55 -30.45 0 5.00e+00 4.00e-02 3.71e+01 dihedral pdb=" CA ARG A 613 " pdb=" C ARG A 613 " pdb=" N ALA A 614 " pdb=" CA ALA A 614 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 4126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 737 0.066 - 0.132: 246 0.132 - 0.199: 53 0.199 - 0.265: 5 0.265 - 0.331: 2 Chirality restraints: 1043 Sorted by residual: chirality pdb=" CG LEU A 520 " pdb=" CB LEU A 520 " pdb=" CD1 LEU A 520 " pdb=" CD2 LEU A 520 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C3' DG C 8 " pdb=" C4' DG C 8 " pdb=" O3' DG C 8 " pdb=" C2' DG C 8 " both_signs ideal model delta sigma weight residual False -2.73 -2.46 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' DT C 9 " pdb=" C4' DT C 9 " pdb=" O3' DT C 9 " pdb=" C2' DT C 9 " both_signs ideal model delta sigma weight residual False -2.73 -2.47 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1040 not shown) Planarity restraints: 1090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 554 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO A 555 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 555 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 555 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 623 " -0.019 2.00e-02 2.50e+03 1.49e-02 5.54e+00 pdb=" CG TRP A 623 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 623 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 623 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 623 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 623 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 623 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 623 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 623 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 623 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA E 13 " -0.027 2.00e-02 2.50e+03 1.36e-02 5.12e+00 pdb=" N9 DA E 13 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DA E 13 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DA E 13 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DA E 13 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA E 13 " -0.008 2.00e-02 2.50e+03 pdb=" N6 DA E 13 " -0.003 2.00e-02 2.50e+03 pdb=" N1 DA E 13 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DA E 13 " -0.013 2.00e-02 2.50e+03 pdb=" N3 DA E 13 " 0.019 2.00e-02 2.50e+03 pdb=" C4 DA E 13 " -0.000 2.00e-02 2.50e+03 ... (remaining 1087 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 47 2.45 - 3.07: 4294 3.07 - 3.68: 10950 3.68 - 4.29: 15651 4.29 - 4.90: 25046 Nonbonded interactions: 55988 Sorted by model distance: nonbonded pdb=" OP2 DT C 1 " pdb="MN MN C 801 " model vdw 1.844 2.320 nonbonded pdb=" OP1 DA C 3 " pdb="MN MN C 801 " model vdw 1.848 2.320 nonbonded pdb=" OP1 DT C 1 " pdb="MN MN C 801 " model vdw 1.918 2.320 nonbonded pdb=" P DT C 1 " pdb="MN MN C 801 " model vdw 2.176 2.680 nonbonded pdb=" OD1 ASN A 746 " pdb=" N ARG A 747 " model vdw 2.272 3.120 ... (remaining 55983 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.950 Find NCS groups from input model: 0.040 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 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 : 0.012 0.121 6963 Z= 0.680 Angle : 1.222 17.493 9537 Z= 0.736 Chirality : 0.068 0.331 1043 Planarity : 0.007 0.064 1090 Dihedral : 16.957 117.560 2735 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.40 % Favored : 92.46 % Rotamer: Outliers : 0.15 % Allowed : 3.89 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.72 (0.24), residues: 743 helix: -2.81 (0.24), residues: 217 sheet: -2.86 (0.40), residues: 110 loop : -2.15 (0.26), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG A 282 TYR 0.031 0.004 TYR A 101 PHE 0.034 0.004 PHE A 540 TRP 0.037 0.006 TRP A 623 HIS 0.020 0.003 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.01189 / 0.68 ( 6963) covalent geometry : angle 1.22233 / 0.74 ( 9537) hydrogen bonds : bond 0.22413 / 14.43 ( 254) hydrogen bonds : angle 9.48863 / 6.67 ( 711) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.271 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 outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.1022 time to fit residues: 24.5935 Evaluate side-chains 116 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 97 ASN A 136 ASN A 240 ASN A 325 ASN A 368 ASN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN A 490 GLN A 602 ASN A 612 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.071969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.055989 restraints weight = 33192.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.058272 restraints weight = 19662.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.059957 restraints weight = 13452.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.061196 restraints weight = 10015.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.062072 restraints weight = 7963.430| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 6963 Z= 0.217 Angle : 0.883 9.055 9537 Z= 0.478 Chirality : 0.054 0.260 1043 Planarity : 0.005 0.039 1090 Dihedral : 20.411 119.963 1196 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.40 % Allowed : 14.37 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.27), residues: 743 helix: -1.47 (0.29), residues: 223 sheet: -2.60 (0.44), residues: 106 loop : -1.71 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 397 TYR 0.034 0.003 TYR A 728 PHE 0.023 0.003 PHE A 380 TRP 0.021 0.003 TRP A 623 HIS 0.006 0.002 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.22 ( 6963) covalent geometry : angle 0.88278 / 0.48 ( 9537) hydrogen bonds : bond 0.07285 / 4.76 ( 254) hydrogen bonds : angle 7.00398 / 4.85 ( 711) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.249 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: A 73 LEU cc_start: 0.8877 (mt) cc_final: 0.8639 (mp) REVERT: A 98 MET cc_start: 0.9039 (mmp) cc_final: 0.8833 (mmp) REVERT: A 169 MET cc_start: 0.8982 (ppp) cc_final: 0.8668 (ppp) REVERT: A 191 MET cc_start: 0.9683 (mmp) cc_final: 0.9402 (mmm) REVERT: A 304 MET cc_start: 0.8669 (mmm) cc_final: 0.7303 (mmp) REVERT: A 353 MET cc_start: 0.8703 (ppp) cc_final: 0.8436 (ppp) REVERT: A 466 MET cc_start: 0.9486 (pmm) cc_final: 0.8781 (mpp) REVERT: A 476 ASN cc_start: 0.9742 (m-40) cc_final: 0.9453 (m-40) REVERT: A 480 LYS cc_start: 0.9671 (mttt) cc_final: 0.9465 (ptpp) REVERT: A 591 PHE cc_start: 0.9745 (m-80) cc_final: 0.9449 (m-80) REVERT: A 731 LYS cc_start: 0.9706 (mttm) cc_final: 0.9385 (mtmm) outliers start: 16 outliers final: 10 residues processed: 141 average time/residue: 0.0741 time to fit residues: 14.1205 Evaluate side-chains 122 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 624 TYR Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 724 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 55 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.070516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.054906 restraints weight = 32993.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.057067 restraints weight = 19744.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.058688 restraints weight = 13569.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.059807 restraints weight = 10194.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.060670 restraints weight = 8180.988| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 6963 Z= 0.189 Angle : 0.775 8.566 9537 Z= 0.419 Chirality : 0.050 0.257 1043 Planarity : 0.004 0.034 1090 Dihedral : 20.038 120.226 1196 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.14 % Allowed : 16.32 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.28), residues: 743 helix: -0.72 (0.32), residues: 230 sheet: -2.54 (0.41), residues: 110 loop : -1.56 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 48 TYR 0.049 0.002 TYR A 728 PHE 0.022 0.002 PHE A 738 TRP 0.012 0.003 TRP A 207 HIS 0.005 0.002 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 ( 6963) covalent geometry : angle 0.77543 / 0.42 ( 9537) hydrogen bonds : bond 0.06181 / 3.97 ( 254) hydrogen bonds : angle 6.43972 / 4.45 ( 711) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.157 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: A 73 LEU cc_start: 0.9026 (mt) cc_final: 0.8381 (mt) REVERT: A 148 LYS cc_start: 0.8057 (mptt) cc_final: 0.7838 (mptt) REVERT: A 169 MET cc_start: 0.9082 (ppp) cc_final: 0.8838 (ppp) REVERT: A 304 MET cc_start: 0.9180 (mmm) cc_final: 0.8430 (mmp) REVERT: A 466 MET cc_start: 0.9543 (pmm) cc_final: 0.8758 (mpp) REVERT: A 476 ASN cc_start: 0.9744 (m-40) cc_final: 0.9505 (m-40) REVERT: A 528 TRP cc_start: 0.8196 (p90) cc_final: 0.7905 (p90) REVERT: A 544 ASP cc_start: 0.8067 (t0) cc_final: 0.7369 (t0) REVERT: A 591 PHE cc_start: 0.9734 (m-80) cc_final: 0.9449 (m-80) REVERT: A 622 ASP cc_start: 0.9508 (t0) cc_final: 0.9281 (p0) REVERT: A 712 ILE cc_start: 0.8846 (mm) cc_final: 0.8631 (tp) REVERT: A 730 ASP cc_start: 0.9478 (t0) cc_final: 0.9107 (m-30) REVERT: A 731 LYS cc_start: 0.9701 (mttm) cc_final: 0.9191 (mtpt) outliers start: 21 outliers final: 12 residues processed: 131 average time/residue: 0.0741 time to fit residues: 13.1622 Evaluate side-chains 117 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 624 TYR Chi-restraints excluded: chain A residue 643 SER Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 724 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 56 optimal weight: 30.0000 chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 0.0370 chunk 24 optimal weight: 2.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.068158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.052933 restraints weight = 34442.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.055017 restraints weight = 20513.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.056582 restraints weight = 14121.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.057672 restraints weight = 10578.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.058526 restraints weight = 8497.982| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 6963 Z= 0.221 Angle : 0.778 8.847 9537 Z= 0.418 Chirality : 0.050 0.290 1043 Planarity : 0.004 0.035 1090 Dihedral : 20.004 119.732 1196 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.25 % Allowed : 19.01 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.28), residues: 743 helix: -0.45 (0.32), residues: 229 sheet: -2.79 (0.41), residues: 106 loop : -1.45 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 747 TYR 0.028 0.002 TYR A 306 PHE 0.016 0.002 PHE A 292 TRP 0.011 0.002 TRP A 528 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.22 ( 6963) covalent geometry : angle 0.77839 / 0.42 ( 9537) hydrogen bonds : bond 0.05615 / 3.59 ( 254) hydrogen bonds : angle 6.27746 / 4.29 ( 711) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.8783 (mt) cc_final: 0.8496 (mt) REVERT: A 138 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8383 (mm) REVERT: A 148 LYS cc_start: 0.8089 (mptt) cc_final: 0.7671 (mptt) REVERT: A 169 MET cc_start: 0.9103 (ppp) cc_final: 0.8839 (ppp) REVERT: A 282 ARG cc_start: 0.9344 (tpp80) cc_final: 0.9081 (tpp80) REVERT: A 297 GLU cc_start: 0.8819 (tp30) cc_final: 0.8372 (tp30) REVERT: A 304 MET cc_start: 0.9177 (mmm) cc_final: 0.8585 (mmm) REVERT: A 324 LEU cc_start: 0.9677 (mt) cc_final: 0.9427 (mp) REVERT: A 353 MET cc_start: 0.8714 (ppp) cc_final: 0.8407 (ppp) REVERT: A 363 MET cc_start: 0.8028 (tpp) cc_final: 0.7714 (tpp) REVERT: A 478 PHE cc_start: 0.8834 (m-10) cc_final: 0.8511 (m-80) REVERT: A 544 ASP cc_start: 0.8201 (t0) cc_final: 0.7674 (t0) REVERT: A 591 PHE cc_start: 0.9744 (m-10) cc_final: 0.9414 (m-80) REVERT: A 622 ASP cc_start: 0.9523 (t0) cc_final: 0.9278 (p0) REVERT: A 730 ASP cc_start: 0.9420 (t0) cc_final: 0.9199 (m-30) REVERT: A 731 LYS cc_start: 0.9611 (mttm) cc_final: 0.9167 (mtpt) outliers start: 15 outliers final: 10 residues processed: 120 average time/residue: 0.0693 time to fit residues: 11.4031 Evaluate side-chains 114 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 624 TYR Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 705 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 58 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 75 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.067457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.052337 restraints weight = 34858.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.054370 restraints weight = 21014.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055913 restraints weight = 14528.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.056962 restraints weight = 10984.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.057781 restraints weight = 8863.739| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 6963 Z= 0.223 Angle : 0.772 12.110 9537 Z= 0.412 Chirality : 0.048 0.236 1043 Planarity : 0.004 0.043 1090 Dihedral : 19.992 119.598 1196 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 22.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.99 % Allowed : 20.21 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.29), residues: 743 helix: -0.25 (0.33), residues: 229 sheet: -2.84 (0.41), residues: 100 loop : -1.38 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 48 TYR 0.034 0.002 TYR A 306 PHE 0.018 0.002 PHE A 628 TRP 0.017 0.002 TRP A 482 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 ( 6963) covalent geometry : angle 0.77205 / 0.41 ( 9537) hydrogen bonds : bond 0.05368 / 3.45 ( 254) hydrogen bonds : angle 6.09797 / 4.20 ( 711) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.153 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: A 73 LEU cc_start: 0.8808 (mt) cc_final: 0.8557 (mt) REVERT: A 98 MET cc_start: 0.9177 (mmt) cc_final: 0.8921 (mmt) REVERT: A 138 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8438 (mm) REVERT: A 148 LYS cc_start: 0.8231 (mptt) cc_final: 0.7813 (mptt) REVERT: A 169 MET cc_start: 0.9097 (ppp) cc_final: 0.8711 (ppp) REVERT: A 282 ARG cc_start: 0.9345 (tpp80) cc_final: 0.8849 (mmm160) REVERT: A 304 MET cc_start: 0.9085 (mmm) cc_final: 0.8422 (mmp) REVERT: A 324 LEU cc_start: 0.9625 (mt) cc_final: 0.9404 (mp) REVERT: A 353 MET cc_start: 0.8666 (ppp) cc_final: 0.8385 (ppp) REVERT: A 363 MET cc_start: 0.8130 (tpp) cc_final: 0.7778 (tpp) REVERT: A 478 PHE cc_start: 0.8872 (m-10) cc_final: 0.8624 (m-80) REVERT: A 544 ASP cc_start: 0.8163 (t0) cc_final: 0.7955 (t0) REVERT: A 591 PHE cc_start: 0.9738 (m-10) cc_final: 0.9387 (m-80) REVERT: A 622 ASP cc_start: 0.9497 (t0) cc_final: 0.9263 (p0) REVERT: A 728 TYR cc_start: 0.9688 (m-10) cc_final: 0.9400 (m-80) REVERT: A 731 LYS cc_start: 0.9620 (mttm) cc_final: 0.9207 (mtpt) outliers start: 20 outliers final: 11 residues processed: 128 average time/residue: 0.0597 time to fit residues: 10.5632 Evaluate side-chains 122 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 705 GLN Chi-restraints excluded: chain A residue 709 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 7 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.067982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.052652 restraints weight = 34933.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.054704 restraints weight = 20979.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.056237 restraints weight = 14546.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.057302 restraints weight = 10984.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.058138 restraints weight = 8886.361| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6963 Z= 0.182 Angle : 0.731 9.639 9537 Z= 0.391 Chirality : 0.047 0.233 1043 Planarity : 0.004 0.038 1090 Dihedral : 19.902 118.910 1196 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.99 % Allowed : 20.21 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.29), residues: 743 helix: 0.03 (0.34), residues: 226 sheet: -2.58 (0.41), residues: 108 loop : -1.21 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 161 TYR 0.037 0.002 TYR A 306 PHE 0.013 0.002 PHE A 380 TRP 0.015 0.002 TRP A 482 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 ( 6963) covalent geometry : angle 0.73099 / 0.39 ( 9537) hydrogen bonds : bond 0.05001 / 3.19 ( 254) hydrogen bonds : angle 5.89989 / 4.04 ( 711) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.148 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: A 98 MET cc_start: 0.9290 (mmt) cc_final: 0.9043 (mmt) REVERT: A 138 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8267 (mm) REVERT: A 148 LYS cc_start: 0.8252 (mptt) cc_final: 0.7787 (mptt) REVERT: A 169 MET cc_start: 0.9062 (ppp) cc_final: 0.8619 (ppp) REVERT: A 282 ARG cc_start: 0.9314 (tpp80) cc_final: 0.8859 (mmm160) REVERT: A 304 MET cc_start: 0.9032 (mmm) cc_final: 0.8346 (mmp) REVERT: A 353 MET cc_start: 0.8736 (ppp) cc_final: 0.8487 (ppp) REVERT: A 363 MET cc_start: 0.8157 (tpp) cc_final: 0.7778 (tpp) REVERT: A 478 PHE cc_start: 0.8808 (m-10) cc_final: 0.8596 (m-80) REVERT: A 591 PHE cc_start: 0.9734 (m-10) cc_final: 0.9436 (m-80) REVERT: A 622 ASP cc_start: 0.9497 (t0) cc_final: 0.9267 (p0) REVERT: A 705 GLN cc_start: 0.9619 (OUTLIER) cc_final: 0.9222 (mt0) REVERT: A 728 TYR cc_start: 0.9681 (m-10) cc_final: 0.9371 (m-80) REVERT: A 731 LYS cc_start: 0.9614 (mttm) cc_final: 0.9179 (mtpt) outliers start: 20 outliers final: 12 residues processed: 123 average time/residue: 0.0631 time to fit residues: 10.5604 Evaluate side-chains 117 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 705 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 31 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.067904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.052711 restraints weight = 34047.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.054760 restraints weight = 20645.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.056297 restraints weight = 14355.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.057365 restraints weight = 10827.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.058191 restraints weight = 8726.853| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6963 Z= 0.175 Angle : 0.740 9.620 9537 Z= 0.390 Chirality : 0.047 0.230 1043 Planarity : 0.005 0.077 1090 Dihedral : 19.857 118.979 1196 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.54 % Allowed : 21.11 % Favored : 76.35 % 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: -1.48 (0.29), residues: 743 helix: 0.05 (0.34), residues: 226 sheet: -2.36 (0.44), residues: 112 loop : -1.12 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 161 TYR 0.032 0.002 TYR A 306 PHE 0.032 0.002 PHE A 628 TRP 0.017 0.002 TRP A 482 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 ( 6963) covalent geometry : angle 0.74044 / 0.39 ( 9537) hydrogen bonds : bond 0.04829 / 3.05 ( 254) hydrogen bonds : angle 5.85745 / 3.97 ( 711) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.9318 (mmt) cc_final: 0.9067 (mmt) REVERT: A 138 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8161 (mm) REVERT: A 148 LYS cc_start: 0.8189 (mptt) cc_final: 0.7730 (mmtm) REVERT: A 169 MET cc_start: 0.9077 (ppp) cc_final: 0.8649 (ppp) REVERT: A 282 ARG cc_start: 0.9313 (tpp80) cc_final: 0.8844 (mmm160) REVERT: A 304 MET cc_start: 0.9047 (mmm) cc_final: 0.8340 (mmp) REVERT: A 353 MET cc_start: 0.8762 (ppp) cc_final: 0.8495 (ppp) REVERT: A 478 PHE cc_start: 0.8832 (m-10) cc_final: 0.8551 (m-80) REVERT: A 591 PHE cc_start: 0.9740 (m-10) cc_final: 0.9464 (m-80) REVERT: A 622 ASP cc_start: 0.9525 (t0) cc_final: 0.9282 (p0) REVERT: A 728 TYR cc_start: 0.9678 (m-10) cc_final: 0.9387 (m-80) REVERT: A 731 LYS cc_start: 0.9593 (mttm) cc_final: 0.9165 (mtpt) outliers start: 17 outliers final: 12 residues processed: 118 average time/residue: 0.0731 time to fit residues: 11.5021 Evaluate side-chains 112 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain A residue 703 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 22 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN A 602 ASN A 711 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.063962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.049558 restraints weight = 37002.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.051497 restraints weight = 22341.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.052918 restraints weight = 15469.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.053923 restraints weight = 11716.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.054660 restraints weight = 9476.507| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 6963 Z= 0.303 Angle : 0.811 8.895 9537 Z= 0.436 Chirality : 0.049 0.239 1043 Planarity : 0.005 0.060 1090 Dihedral : 20.023 119.225 1196 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 29.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.04 % Allowed : 21.86 % Favored : 74.10 % 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: -1.75 (0.29), residues: 743 helix: -0.19 (0.34), residues: 230 sheet: -2.35 (0.43), residues: 113 loop : -1.33 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG A 161 TYR 0.030 0.002 TYR A 306 PHE 0.017 0.003 PHE A 628 TRP 0.017 0.003 TRP A 482 HIS 0.007 0.002 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.30 ( 6963) covalent geometry : angle 0.81089 / 0.44 ( 9537) hydrogen bonds : bond 0.05275 / 3.27 ( 254) hydrogen bonds : angle 6.11894 / 4.15 ( 711) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.9068 (pm20) cc_final: 0.8866 (pm20) REVERT: A 98 MET cc_start: 0.9242 (mmt) cc_final: 0.8997 (mmt) REVERT: A 138 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8468 (mm) REVERT: A 145 ASP cc_start: 0.9332 (p0) cc_final: 0.8934 (p0) REVERT: A 148 LYS cc_start: 0.8329 (mptt) cc_final: 0.8128 (mptt) REVERT: A 169 MET cc_start: 0.9167 (ppp) cc_final: 0.8747 (ppp) REVERT: A 297 GLU cc_start: 0.9003 (tp30) cc_final: 0.8788 (tp30) REVERT: A 304 MET cc_start: 0.9038 (mmm) cc_final: 0.8311 (mmp) REVERT: A 353 MET cc_start: 0.8813 (ppp) cc_final: 0.8555 (ppp) REVERT: A 478 PHE cc_start: 0.9008 (m-10) cc_final: 0.8776 (m-80) REVERT: A 591 PHE cc_start: 0.9738 (m-10) cc_final: 0.9452 (m-80) REVERT: A 622 ASP cc_start: 0.9532 (t0) cc_final: 0.9304 (p0) REVERT: A 694 TYR cc_start: 0.8784 (t80) cc_final: 0.8564 (t80) REVERT: A 728 TYR cc_start: 0.9681 (m-10) cc_final: 0.9418 (m-80) REVERT: A 731 LYS cc_start: 0.9638 (mttm) cc_final: 0.9200 (mtpt) outliers start: 27 outliers final: 17 residues processed: 117 average time/residue: 0.0656 time to fit residues: 10.4245 Evaluate side-chains 111 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 624 TYR Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 720 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 28 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.065770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.050819 restraints weight = 35382.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.052830 restraints weight = 21537.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.054291 restraints weight = 14973.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055403 restraints weight = 11351.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.056221 restraints weight = 9135.170| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6963 Z= 0.179 Angle : 0.767 9.156 9537 Z= 0.408 Chirality : 0.049 0.256 1043 Planarity : 0.004 0.051 1090 Dihedral : 19.847 118.486 1196 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 23.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.95 % Allowed : 25.00 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.30), residues: 743 helix: -0.11 (0.34), residues: 227 sheet: -2.22 (0.46), residues: 111 loop : -1.03 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 161 TYR 0.030 0.002 TYR A 306 PHE 0.015 0.002 PHE A 628 TRP 0.022 0.002 TRP A 482 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 ( 6963) covalent geometry : angle 0.76687 / 0.41 ( 9537) hydrogen bonds : bond 0.04646 / 2.92 ( 254) hydrogen bonds : angle 5.93108 / 3.97 ( 711) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8994 (pm20) cc_final: 0.8790 (pm20) REVERT: A 98 MET cc_start: 0.9250 (mmt) cc_final: 0.9006 (mmt) REVERT: A 138 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8164 (mm) REVERT: A 148 LYS cc_start: 0.8272 (mptt) cc_final: 0.7783 (mptt) REVERT: A 169 MET cc_start: 0.9160 (ppp) cc_final: 0.8725 (ppp) REVERT: A 304 MET cc_start: 0.8999 (mmm) cc_final: 0.8375 (mmm) REVERT: A 353 MET cc_start: 0.8810 (ppp) cc_final: 0.8554 (ppp) REVERT: A 388 PHE cc_start: 0.9027 (m-80) cc_final: 0.8822 (m-80) REVERT: A 478 PHE cc_start: 0.8898 (m-10) cc_final: 0.8547 (m-80) REVERT: A 591 PHE cc_start: 0.9719 (m-10) cc_final: 0.9409 (m-80) REVERT: A 622 ASP cc_start: 0.9506 (t0) cc_final: 0.9269 (p0) REVERT: A 694 TYR cc_start: 0.8770 (t80) cc_final: 0.8550 (t80) REVERT: A 731 LYS cc_start: 0.9639 (mttm) cc_final: 0.9189 (mtpt) outliers start: 13 outliers final: 9 residues processed: 108 average time/residue: 0.0724 time to fit residues: 10.8185 Evaluate side-chains 107 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain A residue 703 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 711 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.067305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.052250 restraints weight = 34511.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054275 restraints weight = 21115.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.055831 restraints weight = 14677.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.056894 restraints weight = 11076.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.057731 restraints weight = 8934.728| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6963 Z= 0.153 Angle : 0.745 9.762 9537 Z= 0.392 Chirality : 0.048 0.228 1043 Planarity : 0.004 0.040 1090 Dihedral : 19.689 119.475 1196 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.65 % Allowed : 25.45 % Favored : 72.90 % 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: -1.43 (0.30), residues: 743 helix: -0.15 (0.34), residues: 227 sheet: -2.07 (0.43), residues: 122 loop : -0.96 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 161 TYR 0.027 0.002 TYR A 306 PHE 0.015 0.002 PHE A 628 TRP 0.021 0.002 TRP A 482 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 6963) covalent geometry : angle 0.74542 / 0.39 ( 9537) hydrogen bonds : bond 0.04384 / 2.78 ( 254) hydrogen bonds : angle 5.81845 / 3.88 ( 711) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.9303 (mmt) cc_final: 0.9080 (mmt) REVERT: A 138 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8141 (mm) REVERT: A 148 LYS cc_start: 0.8133 (mptt) cc_final: 0.7698 (mmtm) REVERT: A 169 MET cc_start: 0.9147 (ppp) cc_final: 0.8702 (ppp) REVERT: A 270 MET cc_start: 0.3451 (pmm) cc_final: 0.3161 (pmm) REVERT: A 304 MET cc_start: 0.9041 (mmm) cc_final: 0.8393 (mmm) REVERT: A 353 MET cc_start: 0.8784 (ppp) cc_final: 0.8512 (ppp) REVERT: A 380 PHE cc_start: 0.9426 (m-80) cc_final: 0.9219 (t80) REVERT: A 478 PHE cc_start: 0.8834 (m-10) cc_final: 0.8468 (m-80) REVERT: A 591 PHE cc_start: 0.9732 (m-10) cc_final: 0.9385 (m-80) REVERT: A 622 ASP cc_start: 0.9524 (t0) cc_final: 0.9278 (p0) REVERT: A 694 TYR cc_start: 0.8745 (t80) cc_final: 0.8507 (t80) REVERT: A 731 LYS cc_start: 0.9604 (mttm) cc_final: 0.9155 (mtpt) outliers start: 11 outliers final: 9 residues processed: 111 average time/residue: 0.0625 time to fit residues: 9.4340 Evaluate side-chains 106 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 681 ASN Chi-restraints excluded: chain A residue 703 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 1 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.8152 > 50:) chunk 58 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN A 705 GLN A 711 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.065453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.050702 restraints weight = 34916.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.052679 restraints weight = 21354.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.054104 restraints weight = 14879.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055192 restraints weight = 11259.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.055999 restraints weight = 9034.121| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6963 Z= 0.194 Angle : 0.769 9.748 9537 Z= 0.409 Chirality : 0.047 0.227 1043 Planarity : 0.005 0.061 1090 Dihedral : 19.741 119.874 1196 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 23.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.80 % Allowed : 26.35 % Favored : 71.86 % 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: -1.42 (0.30), residues: 743 helix: -0.21 (0.34), residues: 227 sheet: -1.93 (0.45), residues: 122 loop : -0.96 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 161 TYR 0.027 0.002 TYR A 306 PHE 0.012 0.002 PHE A 628 TRP 0.016 0.002 TRP A 482 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 ( 6963) covalent geometry : angle 0.76866 / 0.41 ( 9537) hydrogen bonds : bond 0.04586 / 2.95 ( 254) hydrogen bonds : angle 5.86356 / 3.88 ( 711) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1082.39 seconds wall clock time: 19 minutes 31.51 seconds (1171.51 seconds total)