Starting phenix.real_space_refine on Thu Jul 2 05:28:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jh8_61475/07_2026/9jh8_61475.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jh8_61475/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jh8_61475/07_2026/9jh8_61475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jh8_61475/07_2026/9jh8_61475.map" model { file = "/net/cci-nas-00/data/ceres_data/9jh8_61475/07_2026/9jh8_61475.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jh8_61475/07_2026/9jh8_61475.cif" } 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-dev-6108/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, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Time building chain proxies: 1.67, per 1000 atoms: 0.25 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: 0.53 Conformation dependent library (CDL) restraints added in 358.8 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: 0.82 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: 1.20 Time building geometry restraints manager: 0.73 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 3.060 nonbonded pdb=" OP1 DA C 3 " pdb="MN MN C 801 " model vdw 1.848 3.060 nonbonded pdb=" OP1 DT C 1 " pdb="MN MN C 801 " model vdw 1.918 3.060 nonbonded pdb=" P DT C 1 " pdb="MN MN C 801 " model vdw 2.176 3.420 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: 1.120 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.530 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.010 ------------------------------------------------------------------------------- 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= 0.679 Angle : 1.222 17.493 9537 Z= 0.735 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 1.22177 / 0.73 ( 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 : 0.156 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: 0.1001 time to fit residues: 24.1603 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 : 0.249 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.072162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.056182 restraints weight = 32997.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.058493 restraints weight = 19471.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.060184 restraints weight = 13264.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.061422 restraints weight = 9868.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.062375 restraints weight = 7801.878| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 6963 Z= 0.219 Angle : 0.888 10.127 9537 Z= 0.481 Chirality : 0.054 0.246 1043 Planarity : 0.005 0.038 1090 Dihedral : 20.433 118.759 1196 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.54 % Allowed : 14.07 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.27), residues: 743 helix: -1.48 (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 0.008 0.001 ARG A 397 TYR 0.036 0.003 TYR A 728 PHE 0.023 0.003 PHE A 380 TRP 0.023 0.003 TRP A 623 HIS 0.006 0.002 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 ( 6963) covalent geometry : angle 0.88848 / 0.48 ( 9537) hydrogen bonds : bond 0.07221 / 4.72 ( 254) hydrogen bonds : angle 6.98713 / 4.83 ( 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 153 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.243 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: 0.8879 (mt) cc_final: 0.8644 (mp) REVERT: A 98 MET cc_start: 0.9036 (mmp) cc_final: 0.8828 (mmp) REVERT: A 169 MET cc_start: 0.8962 (ppp) cc_final: 0.8629 (ppp) REVERT: A 191 MET cc_start: 0.9682 (mmp) cc_final: 0.9392 (mmm) REVERT: A 304 MET cc_start: 0.8669 (mmm) cc_final: 0.7279 (mmp) REVERT: A 353 MET cc_start: 0.8695 (ppp) cc_final: 0.8429 (ppp) REVERT: A 466 MET cc_start: 0.9465 (pmm) cc_final: 0.8741 (mpp) REVERT: A 476 ASN cc_start: 0.9748 (m-40) cc_final: 0.9462 (m-40) REVERT: A 480 LYS cc_start: 0.9673 (mttt) cc_final: 0.9462 (ptpp) REVERT: A 554 TYR cc_start: 0.7190 (m-80) cc_final: 0.6924 (m-80) REVERT: A 591 PHE cc_start: 0.9740 (m-80) cc_final: 0.9444 (m-80) REVERT: A 622 ASP cc_start: 0.9559 (t0) cc_final: 0.9332 (p0) REVERT: A 652 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8708 (p0) REVERT: A 686 LYS cc_start: 0.9039 (ttmt) cc_final: 0.8656 (mttt) REVERT: A 731 LYS cc_start: 0.9698 (mttm) cc_final: 0.9294 (mtmm) outliers start: 17 outliers final: 10 residues processed: 142 average time/residue: 0.0784 time to fit residues: 15.0114 Evaluate side-chains 126 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 652 ASN 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: 8.9990 chunk 25 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.070775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.055004 restraints weight = 32776.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.057225 restraints weight = 19428.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.058915 restraints weight = 13241.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.060086 restraints weight = 9859.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.060984 restraints weight = 7854.499| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 6963 Z= 0.178 Angle : 0.778 9.450 9537 Z= 0.418 Chirality : 0.051 0.254 1043 Planarity : 0.004 0.034 1090 Dihedral : 20.031 120.017 1196 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.84 % Allowed : 16.17 % Favored : 80.99 % 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: -2.24 (0.28), residues: 743 helix: -0.76 (0.32), residues: 230 sheet: -2.55 (0.42), residues: 112 loop : -1.56 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 48 TYR 0.026 0.002 TYR A 728 PHE 0.022 0.003 PHE A 738 TRP 0.023 0.004 TRP A 207 HIS 0.006 0.002 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 ( 6963) covalent geometry : angle 0.77767 / 0.42 ( 9537) hydrogen bonds : bond 0.06145 / 3.94 ( 254) hydrogen bonds : angle 6.45284 / 4.46 ( 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: 19 poor density : 122 time to evaluate : 0.262 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: 0.8994 (mt) cc_final: 0.8320 (mt) REVERT: A 148 LYS cc_start: 0.8100 (mptt) cc_final: 0.7854 (mptt) REVERT: A 169 MET cc_start: 0.9063 (ppp) cc_final: 0.8850 (ppp) REVERT: A 191 MET cc_start: 0.9648 (mmp) cc_final: 0.9395 (mmm) REVERT: A 304 MET cc_start: 0.9236 (mmm) cc_final: 0.8468 (mmp) REVERT: A 352 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9369 (tp) REVERT: A 466 MET cc_start: 0.9543 (pmm) cc_final: 0.8739 (mpp) REVERT: A 476 ASN cc_start: 0.9741 (m-40) cc_final: 0.9527 (m-40) REVERT: A 544 ASP cc_start: 0.8004 (t0) cc_final: 0.7256 (t0) REVERT: A 591 PHE cc_start: 0.9738 (m-80) cc_final: 0.9450 (m-80) REVERT: A 622 ASP cc_start: 0.9528 (t0) cc_final: 0.9298 (p0) REVERT: A 728 TYR cc_start: 0.9658 (m-80) cc_final: 0.9069 (m-80) REVERT: A 730 ASP cc_start: 0.9356 (t0) cc_final: 0.9070 (m-30) REVERT: A 731 LYS cc_start: 0.9583 (mttm) cc_final: 0.9145 (mtpt) outliers start: 19 outliers final: 11 residues processed: 131 average time/residue: 0.0873 time to fit residues: 15.3581 Evaluate side-chains 119 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 352 LEU 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: 9.9990 chunk 20 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 56 optimal weight: 0.0370 chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 57 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 chunk 24 optimal weight: 5.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.071915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.056047 restraints weight = 33039.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.058282 restraints weight = 19792.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.059906 restraints weight = 13643.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.061170 restraints weight = 10263.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.062007 restraints weight = 8178.703| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6963 Z= 0.162 Angle : 0.771 8.880 9537 Z= 0.406 Chirality : 0.050 0.283 1043 Planarity : 0.004 0.039 1090 Dihedral : 19.852 118.997 1196 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.25 % Allowed : 19.46 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.99 (0.29), residues: 743 helix: -0.56 (0.32), residues: 229 sheet: -2.35 (0.47), residues: 100 loop : -1.46 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 747 TYR 0.030 0.002 TYR A 306 PHE 0.015 0.002 PHE A 292 TRP 0.010 0.002 TRP A 482 HIS 0.004 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 6963) covalent geometry : angle 0.77090 / 0.41 ( 9537) hydrogen bonds : bond 0.05545 / 3.56 ( 254) hydrogen bonds : angle 6.10292 / 4.19 ( 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 136 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.250 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: A 57 PHE cc_start: 0.9265 (m-10) cc_final: 0.9050 (m-80) REVERT: A 73 LEU cc_start: 0.8888 (mt) cc_final: 0.8362 (mp) REVERT: A 98 MET cc_start: 0.9024 (mmt) cc_final: 0.8786 (mmt) REVERT: A 169 MET cc_start: 0.9060 (ppp) cc_final: 0.8796 (ppp) REVERT: A 191 MET cc_start: 0.9643 (mmp) cc_final: 0.9403 (mmm) REVERT: A 282 ARG cc_start: 0.9367 (tpp80) cc_final: 0.8804 (mmm160) REVERT: A 304 MET cc_start: 0.9110 (mmm) cc_final: 0.8605 (mmm) REVERT: A 353 MET cc_start: 0.8487 (ppp) cc_final: 0.8235 (ppp) REVERT: A 491 MET cc_start: 0.8660 (ptp) cc_final: 0.8102 (pmm) REVERT: A 544 ASP cc_start: 0.7838 (t0) cc_final: 0.7072 (t0) REVERT: A 591 PHE cc_start: 0.9745 (m-10) cc_final: 0.9425 (m-80) REVERT: A 622 ASP cc_start: 0.9504 (t0) cc_final: 0.9243 (p0) REVERT: A 728 TYR cc_start: 0.9630 (m-10) cc_final: 0.9350 (m-80) REVERT: A 730 ASP cc_start: 0.9284 (t0) cc_final: 0.9027 (m-30) REVERT: A 731 LYS cc_start: 0.9579 (mttm) cc_final: 0.9179 (mtpt) outliers start: 15 outliers final: 10 residues processed: 128 average time/residue: 0.0739 time to fit residues: 12.9456 Evaluate side-chains 117 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 133 ILE 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 628 PHE 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: 1.9990 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.071584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.055700 restraints weight = 32965.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.057954 restraints weight = 19648.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.059597 restraints weight = 13438.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.060754 restraints weight = 10059.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.061643 restraints weight = 8070.378| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6963 Z= 0.161 Angle : 0.759 13.712 9537 Z= 0.400 Chirality : 0.049 0.241 1043 Planarity : 0.004 0.056 1090 Dihedral : 19.797 119.653 1196 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.44 % Allowed : 19.61 % Favored : 76.95 % 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 (0.29), residues: 743 helix: -0.14 (0.34), residues: 226 sheet: -2.24 (0.47), residues: 100 loop : -1.27 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 161 TYR 0.039 0.002 TYR A 306 PHE 0.017 0.002 PHE A 478 TRP 0.013 0.002 TRP A 482 HIS 0.005 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 6963) covalent geometry : angle 0.75918 / 0.40 ( 9537) hydrogen bonds : bond 0.05170 / 3.32 ( 254) hydrogen bonds : angle 5.88635 / 4.01 ( 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 138 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.259 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: 0.8855 (mt) cc_final: 0.8490 (mt) REVERT: A 98 MET cc_start: 0.9167 (mmt) cc_final: 0.8787 (mmt) REVERT: A 148 LYS cc_start: 0.8336 (mmtm) cc_final: 0.7942 (mptt) REVERT: A 169 MET cc_start: 0.9109 (ppp) cc_final: 0.8839 (ppp) REVERT: A 191 MET cc_start: 0.9632 (mmp) cc_final: 0.9425 (mmm) REVERT: A 304 MET cc_start: 0.9125 (mmm) cc_final: 0.8497 (mmm) REVERT: A 353 MET cc_start: 0.8698 (ppp) cc_final: 0.8475 (ppp) REVERT: A 363 MET cc_start: 0.7816 (tpp) cc_final: 0.7544 (tpp) REVERT: A 491 MET cc_start: 0.8568 (ptp) cc_final: 0.8011 (pmm) REVERT: A 544 ASP cc_start: 0.7763 (t0) cc_final: 0.7528 (t0) REVERT: A 591 PHE cc_start: 0.9752 (m-10) cc_final: 0.9420 (m-80) REVERT: A 620 ASP cc_start: 0.9078 (m-30) cc_final: 0.8594 (p0) REVERT: A 705 GLN cc_start: 0.9624 (OUTLIER) cc_final: 0.9352 (mt0) REVERT: A 728 TYR cc_start: 0.9666 (m-10) cc_final: 0.9387 (m-80) REVERT: A 730 ASP cc_start: 0.9285 (t0) cc_final: 0.9055 (m-30) REVERT: A 731 LYS cc_start: 0.9575 (mttm) cc_final: 0.9168 (mtpt) outliers start: 23 outliers final: 12 residues processed: 128 average time/residue: 0.0740 time to fit residues: 13.0022 Evaluate side-chains 118 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 181 ASP 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 648 ILE 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 Chi-restraints excluded: chain A residue 717 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 7 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 ASN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN A 655 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.064673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.050224 restraints weight = 36779.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.052170 restraints weight = 21948.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.053611 restraints weight = 15131.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.054599 restraints weight = 11396.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.055373 restraints weight = 9224.306| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.136 6963 Z= 0.368 Angle : 0.873 10.980 9537 Z= 0.472 Chirality : 0.049 0.226 1043 Planarity : 0.005 0.044 1090 Dihedral : 20.082 119.776 1196 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 30.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.04 % Allowed : 20.21 % Favored : 75.75 % 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: -1.90 (0.28), residues: 743 helix: -0.31 (0.32), residues: 230 sheet: -2.38 (0.43), residues: 108 loop : -1.48 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 161 TYR 0.032 0.003 TYR A 306 PHE 0.020 0.004 PHE A 628 TRP 0.011 0.003 TRP A 482 HIS 0.007 0.002 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00750 / 0.37 ( 6963) covalent geometry : angle 0.87295 / 0.47 ( 9537) hydrogen bonds : bond 0.05872 / 3.66 ( 254) hydrogen bonds : angle 6.25879 / 4.29 ( 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 132 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8928 (mmt) cc_final: 0.8669 (mmt) REVERT: A 145 ASP cc_start: 0.9306 (p0) cc_final: 0.8887 (p0) REVERT: A 148 LYS cc_start: 0.8539 (mmtm) cc_final: 0.8071 (mptt) REVERT: A 282 ARG cc_start: 0.9359 (tpp80) cc_final: 0.8886 (mmm160) REVERT: A 304 MET cc_start: 0.9001 (mmm) cc_final: 0.8302 (mmp) REVERT: A 353 MET cc_start: 0.8715 (ppp) cc_final: 0.8451 (ppp) REVERT: A 544 ASP cc_start: 0.8289 (t0) cc_final: 0.7978 (t0) REVERT: A 591 PHE cc_start: 0.9752 (m-10) cc_final: 0.9470 (m-80) REVERT: A 622 ASP cc_start: 0.9472 (t70) cc_final: 0.9228 (p0) REVERT: A 639 GLU cc_start: 0.9507 (mt-10) cc_final: 0.9287 (mm-30) REVERT: A 705 GLN cc_start: 0.9614 (OUTLIER) cc_final: 0.9307 (mt0) REVERT: A 728 TYR cc_start: 0.9637 (m-10) cc_final: 0.9392 (m-80) REVERT: A 731 LYS cc_start: 0.9642 (mttm) cc_final: 0.9237 (mtpt) outliers start: 27 outliers final: 20 residues processed: 117 average time/residue: 0.0797 time to fit residues: 12.4815 Evaluate side-chains 119 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 104 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 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 647 LYS Chi-restraints excluded: chain A residue 648 ILE 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 Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 737 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.067891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.052823 restraints weight = 34261.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.054919 restraints weight = 20478.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.056418 restraints weight = 14082.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.057527 restraints weight = 10584.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.058289 restraints weight = 8508.667| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6963 Z= 0.161 Angle : 0.776 11.282 9537 Z= 0.407 Chirality : 0.049 0.234 1043 Planarity : 0.005 0.062 1090 Dihedral : 19.879 117.937 1196 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.54 % Allowed : 23.35 % 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: -1.44 (0.29), residues: 743 helix: -0.15 (0.33), residues: 228 sheet: -1.94 (0.51), residues: 92 loop : -1.15 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 161 TYR 0.038 0.002 TYR A 306 PHE 0.017 0.002 PHE A 380 TRP 0.019 0.002 TRP A 482 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 6963) covalent geometry : angle 0.77617 / 0.41 ( 9537) hydrogen bonds : bond 0.04777 / 3.03 ( 254) hydrogen bonds : angle 5.96980 / 4.04 ( 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 121 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.151 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: A 73 LEU cc_start: 0.8885 (mt) cc_final: 0.8579 (mp) REVERT: A 148 LYS cc_start: 0.8556 (mmtm) cc_final: 0.8075 (mptt) REVERT: A 304 MET cc_start: 0.9047 (mmm) cc_final: 0.8406 (mmm) REVERT: A 353 MET cc_start: 0.8741 (ppp) cc_final: 0.8497 (ppp) REVERT: A 491 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8239 (mpp) REVERT: A 591 PHE cc_start: 0.9731 (m-10) cc_final: 0.9427 (m-80) REVERT: A 622 ASP cc_start: 0.9431 (t70) cc_final: 0.9157 (p0) REVERT: A 639 GLU cc_start: 0.9500 (mt-10) cc_final: 0.9291 (mm-30) REVERT: A 728 TYR cc_start: 0.9651 (m-10) cc_final: 0.9336 (m-80) REVERT: A 731 LYS cc_start: 0.9600 (mttm) cc_final: 0.9159 (mtpt) outliers start: 17 outliers final: 11 residues processed: 112 average time/residue: 0.0703 time to fit residues: 10.4789 Evaluate side-chains 111 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL 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 529 VAL Chi-restraints excluded: chain A residue 624 TYR Chi-restraints excluded: chain A residue 628 PHE 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: 0.6980 chunk 61 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN A 711 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.065929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.051281 restraints weight = 35925.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.053274 restraints weight = 21451.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.054730 restraints weight = 14782.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.055748 restraints weight = 11148.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.056533 restraints weight = 8997.042| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 6963 Z= 0.223 Angle : 0.785 10.618 9537 Z= 0.417 Chirality : 0.048 0.224 1043 Planarity : 0.005 0.070 1090 Dihedral : 19.882 119.033 1196 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 24.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.95 % Allowed : 25.15 % 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: -1.57 (0.30), residues: 743 helix: -0.28 (0.34), residues: 229 sheet: -2.04 (0.47), residues: 108 loop : -1.16 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 161 TYR 0.034 0.002 TYR A 306 PHE 0.069 0.003 PHE A 478 TRP 0.019 0.003 TRP A 482 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.22 ( 6963) covalent geometry : angle 0.78541 / 0.42 ( 9537) hydrogen bonds : bond 0.04788 / 3.01 ( 254) hydrogen bonds : angle 6.16026 / 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 113 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.9259 (p0) cc_final: 0.8830 (p0) REVERT: A 148 LYS cc_start: 0.8577 (mmtm) cc_final: 0.8123 (mptt) REVERT: A 282 ARG cc_start: 0.9282 (tpp80) cc_final: 0.8859 (mmm160) REVERT: A 304 MET cc_start: 0.9057 (mmm) cc_final: 0.8424 (mmm) REVERT: A 353 MET cc_start: 0.8809 (ppp) cc_final: 0.8546 (ppp) REVERT: A 491 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8219 (ptp) REVERT: A 591 PHE cc_start: 0.9746 (m-10) cc_final: 0.9450 (m-80) REVERT: A 622 ASP cc_start: 0.9450 (t70) cc_final: 0.9185 (p0) REVERT: A 639 GLU cc_start: 0.9526 (mt-10) cc_final: 0.9305 (mm-30) REVERT: A 694 TYR cc_start: 0.8801 (t80) cc_final: 0.8586 (t80) REVERT: A 728 TYR cc_start: 0.9659 (m-10) cc_final: 0.9402 (m-80) REVERT: A 731 LYS cc_start: 0.9615 (mttm) cc_final: 0.9194 (mtpt) outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 0.0793 time to fit residues: 11.5322 Evaluate side-chains 108 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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 441 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 529 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 28 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 27 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 overall best weight: 1.9744 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.066501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.051630 restraints weight = 34968.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.053694 restraints weight = 21003.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.055176 restraints weight = 14479.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.056271 restraints weight = 10866.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.057051 restraints weight = 8713.506| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6963 Z= 0.183 Angle : 0.782 12.924 9537 Z= 0.414 Chirality : 0.049 0.218 1043 Planarity : 0.005 0.063 1090 Dihedral : 19.807 118.550 1196 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.25 % Allowed : 25.45 % Favored : 72.31 % 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: -1.55 (0.30), residues: 743 helix: -0.33 (0.34), residues: 229 sheet: -1.93 (0.45), residues: 119 loop : -1.09 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 161 TYR 0.033 0.002 TYR A 306 PHE 0.061 0.002 PHE A 478 TRP 0.018 0.002 TRP A 482 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 6963) covalent geometry : angle 0.78200 / 0.41 ( 9537) hydrogen bonds : bond 0.04586 / 2.94 ( 254) hydrogen bonds : angle 6.14767 / 4.09 ( 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 118 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.193 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: 0.8978 (mt) cc_final: 0.8646 (mp) REVERT: A 148 LYS cc_start: 0.8644 (mmtm) cc_final: 0.8226 (mptt) REVERT: A 282 ARG cc_start: 0.9249 (tpp80) cc_final: 0.8859 (mmm160) REVERT: A 304 MET cc_start: 0.9040 (mmm) cc_final: 0.8474 (mmm) REVERT: A 353 MET cc_start: 0.8803 (ppp) cc_final: 0.8537 (ppp) REVERT: A 480 LYS cc_start: 0.9623 (pttm) cc_final: 0.9309 (mtmm) REVERT: A 491 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8053 (mpp) REVERT: A 498 GLU cc_start: 0.9504 (mp0) cc_final: 0.9275 (pm20) REVERT: A 591 PHE cc_start: 0.9735 (m-10) cc_final: 0.9427 (m-80) REVERT: A 622 ASP cc_start: 0.9443 (t70) cc_final: 0.9178 (p0) REVERT: A 639 GLU cc_start: 0.9520 (mt-10) cc_final: 0.9301 (mm-30) REVERT: A 694 TYR cc_start: 0.8796 (t80) cc_final: 0.8570 (t80) REVERT: A 728 TYR cc_start: 0.9671 (m-10) cc_final: 0.9410 (m-80) REVERT: A 731 LYS cc_start: 0.9603 (mttm) cc_final: 0.9176 (mtpt) outliers start: 15 outliers final: 9 residues processed: 113 average time/residue: 0.0780 time to fit residues: 12.0145 Evaluate side-chains 109 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 460 ILE Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 628 PHE 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: 4.9990 chunk 31 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.066328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.051537 restraints weight = 35527.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.053548 restraints weight = 21406.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.055005 restraints weight = 14817.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.056092 restraints weight = 11167.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.056868 restraints weight = 8977.847| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.5154 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= 0.196 Angle : 0.777 10.053 9537 Z= 0.414 Chirality : 0.049 0.215 1043 Planarity : 0.005 0.060 1090 Dihedral : 19.801 118.895 1196 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.80 % Allowed : 25.90 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.44 (0.30), residues: 743 helix: -0.34 (0.34), residues: 228 sheet: -1.66 (0.48), residues: 109 loop : -1.06 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 161 TYR 0.028 0.002 TYR A 306 PHE 0.056 0.002 PHE A 478 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 0.00413 / 0.20 ( 6963) covalent geometry : angle 0.77703 / 0.41 ( 9537) hydrogen bonds : bond 0.04658 / 3.02 ( 254) hydrogen bonds : angle 6.08460 / 4.04 ( 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 111 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.242 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: A 148 LYS cc_start: 0.8656 (mmtm) cc_final: 0.8235 (mptt) REVERT: A 270 MET cc_start: 0.3311 (pmm) cc_final: 0.3014 (pmm) REVERT: A 282 ARG cc_start: 0.9240 (tpp80) cc_final: 0.8862 (mmm160) REVERT: A 304 MET cc_start: 0.9041 (mmm) cc_final: 0.8552 (mmm) REVERT: A 353 MET cc_start: 0.8794 (ppp) cc_final: 0.8529 (ppp) REVERT: A 380 PHE cc_start: 0.9462 (m-80) cc_final: 0.9182 (t80) REVERT: A 491 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8011 (mpp) REVERT: A 591 PHE cc_start: 0.9735 (m-10) cc_final: 0.9430 (m-80) REVERT: A 622 ASP cc_start: 0.9444 (t70) cc_final: 0.9181 (p0) REVERT: A 639 GLU cc_start: 0.9525 (mt-10) cc_final: 0.9314 (mm-30) REVERT: A 694 TYR cc_start: 0.8791 (t80) cc_final: 0.8551 (t80) REVERT: A 711 GLN cc_start: 0.9378 (mt0) cc_final: 0.9117 (mt0) REVERT: A 731 LYS cc_start: 0.9595 (mttm) cc_final: 0.9121 (mtpt) outliers start: 12 outliers final: 9 residues processed: 106 average time/residue: 0.0753 time to fit residues: 10.7826 Evaluate side-chains 108 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 460 ILE Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 628 PHE 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: 0.9990 chunk 19 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 0.2980 chunk 26 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.067620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.052290 restraints weight = 33688.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054388 restraints weight = 20309.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.055938 restraints weight = 13970.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.057018 restraints weight = 10490.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.057837 restraints weight = 8425.674| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6963 Z= 0.153 Angle : 0.796 11.406 9537 Z= 0.417 Chirality : 0.049 0.213 1043 Planarity : 0.004 0.063 1090 Dihedral : 19.687 119.001 1196 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.80 % Allowed : 25.90 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.30), residues: 743 helix: -0.17 (0.34), residues: 227 sheet: -1.49 (0.49), residues: 109 loop : -0.93 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 161 TYR 0.039 0.002 TYR A 306 PHE 0.054 0.002 PHE A 478 TRP 0.018 0.002 TRP A 482 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 6963) covalent geometry : angle 0.79617 / 0.42 ( 9537) hydrogen bonds : bond 0.04413 / 2.91 ( 254) hydrogen bonds : angle 5.98995 / 3.97 ( 711) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1166.19 seconds wall clock time: 20 minutes 59.49 seconds (1259.49 seconds total)