Starting phenix.real_space_refine on Thu Jul 2 04:57:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0j_45086/07_2026/9c0j_45086.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0j_45086/07_2026/9c0j_45086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c0j_45086/07_2026/9c0j_45086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0j_45086/07_2026/9c0j_45086.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c0j_45086/07_2026/9c0j_45086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0j_45086/07_2026/9c0j_45086.map" } resolution = 3.17 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= -0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 167 5.49 5 Mg 1 5.21 5 S 13 5.16 5 C 3809 2.51 5 N 1240 2.21 5 O 1779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s 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: 7010 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3481 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 13, 'TRANS': 411} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "R" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3313 Classifications: {'RNA': 155} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 10, 'rna3p_pur': 67, 'rna3p_pyr': 61} Link IDs: {'rna2p': 26, 'rna3p': 128} Chain breaks: 4 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Time building chain proxies: 1.78, per 1000 atoms: 0.25 Number of scatterers: 7010 At special positions: 0 Unit cell: (131.716, 110.5, 79.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 S 13 16.00 P 167 15.00 Mg 1 11.99 O 1779 8.00 N 1240 7.00 C 3809 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: 0.56 Conformation dependent library (CDL) restraints added in 255.0 milliseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 814 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 53.4% alpha, 13.6% beta 58 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 removed outlier: 3.603A pdb=" N LYS A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 removed outlier: 3.630A pdb=" N ILE A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 38 " --> pdb=" O GLU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 101 removed outlier: 4.132A pdb=" N GLY A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 149 through 162 Processing helix chain 'A' and resid 167 through 179 Processing helix chain 'A' and resid 185 through 193 Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 237 through 246 removed outlier: 3.731A pdb=" N MET A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 260 removed outlier: 3.728A pdb=" N ARG A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.772A pdb=" N ALA A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 Processing helix chain 'A' and resid 336 through 368 removed outlier: 3.865A pdb=" N LEU A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 385 Processing helix chain 'A' and resid 391 through 403 Processing helix chain 'A' and resid 405 through 413 removed outlier: 3.937A pdb=" N LYS A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 425 Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 74 removed outlier: 3.780A pdb=" N ARG A 70 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 49 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE A 44 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 267 removed outlier: 3.645A pdb=" N CYS A 134 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 314 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 323 181 hydrogen bonds defined for protein. 516 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 140 hydrogen bonds 236 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 816 1.32 - 1.44: 2984 1.44 - 1.56: 3337 1.56 - 1.68: 334 1.68 - 1.81: 22 Bond restraints: 7493 Sorted by residual: bond pdb=" C1' DT P 8 " pdb=" N1 DT P 8 " ideal model delta sigma weight residual 1.468 1.568 -0.100 1.40e-02 5.10e+03 5.11e+01 bond pdb=" C1' DT P 5 " pdb=" N1 DT P 5 " ideal model delta sigma weight residual 1.468 1.567 -0.099 1.40e-02 5.10e+03 4.95e+01 bond pdb=" O3B TTP A 502 " pdb=" PG TTP A 502 " ideal model delta sigma weight residual 1.748 1.608 0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" N1 DT P 5 " pdb=" C2 DT P 5 " ideal model delta sigma weight residual 1.376 1.415 -0.039 8.00e-03 1.56e+04 2.42e+01 bond pdb=" N9 A R 201 " pdb=" C4 A R 201 " ideal model delta sigma weight residual 1.374 1.396 -0.022 6.00e-03 2.78e+04 1.29e+01 ... (remaining 7488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 10300 2.04 - 4.08: 470 4.08 - 6.13: 89 6.13 - 8.17: 27 8.17 - 10.21: 11 Bond angle restraints: 10897 Sorted by residual: angle pdb=" O4' DT P 5 " pdb=" C1' DT P 5 " pdb=" N1 DT P 5 " ideal model delta sigma weight residual 108.00 114.48 -6.48 7.00e-01 2.04e+00 8.58e+01 angle pdb=" C1' U R 268 " pdb=" N1 U R 268 " pdb=" C2 U R 268 " ideal model delta sigma weight residual 117.70 125.53 -7.83 1.20e+00 6.94e-01 4.25e+01 angle pdb=" C1' C R 269 " pdb=" N1 C R 269 " pdb=" C2 C R 269 " ideal model delta sigma weight residual 118.80 125.87 -7.07 1.10e+00 8.26e-01 4.13e+01 angle pdb=" C2 C R 2 " pdb=" N1 C R 2 " pdb=" C6 C R 2 " ideal model delta sigma weight residual 120.30 117.84 2.46 4.00e-01 6.25e+00 3.77e+01 angle pdb=" C1' U R 224 " pdb=" N1 U R 224 " pdb=" C2 U R 224 " ideal model delta sigma weight residual 117.70 124.88 -7.18 1.20e+00 6.94e-01 3.58e+01 ... (remaining 10892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.53: 4097 26.53 - 53.07: 366 53.07 - 79.60: 231 79.60 - 106.14: 13 106.14 - 132.67: 3 Dihedral angle restraints: 4710 sinusoidal: 3447 harmonic: 1263 Sorted by residual: dihedral pdb=" O4' U R 134 " pdb=" C1' U R 134 " pdb=" N1 U R 134 " pdb=" C2 U R 134 " ideal model delta sinusoidal sigma weight residual -160.00 -67.13 -92.87 1 1.50e+01 4.44e-03 4.48e+01 dihedral pdb=" O4' A R 201 " pdb=" C1' A R 201 " pdb=" N9 A R 201 " pdb=" C4 A R 201 " ideal model delta sinusoidal sigma weight residual 68.00 149.95 -81.95 1 1.70e+01 3.46e-03 2.86e+01 dihedral pdb=" CA ASP A 312 " pdb=" C ASP A 312 " pdb=" N SER A 313 " pdb=" CA SER A 313 " ideal model delta harmonic sigma weight residual 180.00 154.59 25.41 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 4707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1152 0.073 - 0.145: 146 0.145 - 0.218: 21 0.218 - 0.291: 4 0.291 - 0.363: 1 Chirality restraints: 1324 Sorted by residual: chirality pdb=" C3' A R 210 " pdb=" C4' A R 210 " pdb=" O3' A R 210 " pdb=" C2' A R 210 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" C1' U R 173 " pdb=" O4' U R 173 " pdb=" C2' U R 173 " pdb=" N1 U R 173 " both_signs ideal model delta sigma weight residual False 2.47 2.18 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C1' U R 224 " pdb=" O4' U R 224 " pdb=" C2' U R 224 " pdb=" N1 U R 224 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 1321 not shown) Planarity restraints: 771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 254 " -0.226 9.50e-02 1.11e+02 1.02e-01 7.97e+00 pdb=" NE ARG A 254 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 254 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG A 254 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 254 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 302 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C LYS A 302 " 0.046 2.00e-02 2.50e+03 pdb=" O LYS A 302 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 303 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 204 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C ARG A 204 " 0.046 2.00e-02 2.50e+03 pdb=" O ARG A 204 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS A 205 " -0.016 2.00e-02 2.50e+03 ... (remaining 768 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.71: 374 2.71 - 3.32: 6416 3.32 - 3.92: 15484 3.92 - 4.53: 20134 4.53 - 5.14: 27208 Nonbonded interactions: 69616 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O1B TTP A 502 " model vdw 2.099 2.170 nonbonded pdb=" OD2 ASP A 269 " pdb="MG MG A 501 " model vdw 2.119 2.170 nonbonded pdb=" O LEU A 141 " pdb="MG MG A 501 " model vdw 2.307 2.170 nonbonded pdb=" O TYR A 381 " pdb=" OG SER A 385 " model vdw 2.365 3.040 nonbonded pdb=" OH TYR A 86 " pdb=" OD2 ASP A 169 " model vdw 2.385 3.040 ... (remaining 69611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.240 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 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 : 0.006 0.140 7493 Z= 0.406 Angle : 1.064 10.208 10897 Z= 0.924 Chirality : 0.052 0.363 1324 Planarity : 0.009 0.102 771 Dihedral : 21.848 132.671 3896 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.80 % Allowed : 4.29 % Favored : 94.91 % 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: -0.50 (0.36), residues: 423 helix: -0.83 (0.29), residues: 209 sheet: 1.28 (0.67), residues: 55 loop : 0.07 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG A 254 TYR 0.021 0.003 TYR A 89 PHE 0.021 0.003 PHE A 212 TRP 0.013 0.002 TRP A 8 HIS 0.006 0.002 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.41 ( 7493) covalent geometry : angle 1.06384 / 0.92 (10897) hydrogen bonds : bond 0.15167 / 10.36 ( 321) hydrogen bonds : angle 5.62385 / 3.92 ( 752) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.176 Fit side-chains REVERT: A 198 ASN cc_start: 0.8565 (t0) cc_final: 0.8306 (t0) REVERT: A 205 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8059 (mtpp) REVERT: A 246 MET cc_start: 0.8827 (mmm) cc_final: 0.8616 (mmt) REVERT: A 259 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7290 (mt-10) REVERT: A 319 MET cc_start: 0.8333 (mtm) cc_final: 0.7991 (mtp) REVERT: A 329 ASP cc_start: 0.8330 (p0) cc_final: 0.8073 (p0) outliers start: 3 outliers final: 1 residues processed: 59 average time/residue: 0.1643 time to fit residues: 11.5202 Evaluate side-chains 42 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 296 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 50.0000 chunk 56 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.0970 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.166717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.115220 restraints weight = 7011.282| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 0.69 r_work: 0.2769 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7493 Z= 0.144 Angle : 0.550 6.375 10897 Z= 0.339 Chirality : 0.040 0.234 1324 Planarity : 0.005 0.034 771 Dihedral : 22.732 131.470 3014 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.07 % Allowed : 5.09 % Favored : 93.83 % 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: 0.76 (0.39), residues: 423 helix: 0.73 (0.34), residues: 214 sheet: 1.34 (0.69), residues: 53 loop : 0.08 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 254 TYR 0.014 0.001 TYR A 245 PHE 0.011 0.002 PHE A 47 TRP 0.005 0.001 TRP A 157 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 7493) covalent geometry : angle 0.54985 / 0.34 (10897) hydrogen bonds : bond 0.06836 / 4.20 ( 321) hydrogen bonds : angle 3.79863 / 2.66 ( 752) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.190 Fit side-chains REVERT: A 198 ASN cc_start: 0.8676 (t0) cc_final: 0.8288 (t0) REVERT: A 205 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8076 (mtpp) REVERT: A 259 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7677 (mt-10) REVERT: A 319 MET cc_start: 0.8727 (mtm) cc_final: 0.8348 (mtp) REVERT: A 352 ARG cc_start: 0.8576 (ttm-80) cc_final: 0.7939 (mtt90) outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.1367 time to fit residues: 7.7775 Evaluate side-chains 47 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 0.0000 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 4 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 53 optimal weight: 30.0000 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.168828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.117165 restraints weight = 7017.190| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 0.77 r_work: 0.2834 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7493 Z= 0.110 Angle : 0.471 6.179 10897 Z= 0.297 Chirality : 0.036 0.242 1324 Planarity : 0.004 0.032 771 Dihedral : 22.595 130.348 3013 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.34 % Allowed : 8.31 % Favored : 90.35 % 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: 1.55 (0.40), residues: 423 helix: 1.52 (0.35), residues: 212 sheet: 1.69 (0.67), residues: 53 loop : 0.22 (0.47), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 254 TYR 0.009 0.001 TYR A 245 PHE 0.007 0.001 PHE A 52 TRP 0.007 0.001 TRP A 157 HIS 0.002 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.11 ( 7493) covalent geometry : angle 0.47083 / 0.30 (10897) hydrogen bonds : bond 0.05721 / 3.44 ( 321) hydrogen bonds : angle 3.43822 / 2.44 ( 752) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.225 Fit side-chains REVERT: A 198 ASN cc_start: 0.8620 (t0) cc_final: 0.8196 (t0) REVERT: A 205 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.7972 (mtpp) REVERT: A 259 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7625 (mt-10) REVERT: A 352 ARG cc_start: 0.8540 (ttm-80) cc_final: 0.7987 (mtt90) outliers start: 5 outliers final: 2 residues processed: 48 average time/residue: 0.1521 time to fit residues: 8.8812 Evaluate side-chains 45 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 25 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN A 386 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.161833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.108661 restraints weight = 7116.871| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 0.79 r_work: 0.2670 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 7493 Z= 0.246 Angle : 0.600 8.461 10897 Z= 0.351 Chirality : 0.043 0.247 1324 Planarity : 0.005 0.035 771 Dihedral : 22.592 133.204 3013 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.14 % Allowed : 8.58 % Favored : 89.28 % 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: 0.85 (0.39), residues: 423 helix: 1.16 (0.35), residues: 214 sheet: 0.79 (0.63), residues: 63 loop : -0.30 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 306 TYR 0.019 0.002 TYR A 245 PHE 0.012 0.002 PHE A 328 TRP 0.012 0.002 TRP A 157 HIS 0.005 0.002 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.25 ( 7493) covalent geometry : angle 0.59987 / 0.35 (10897) hydrogen bonds : bond 0.07334 / 4.50 ( 321) hydrogen bonds : angle 3.61644 / 2.56 ( 752) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.215 Fit side-chains REVERT: A 352 ARG cc_start: 0.8534 (ttm-80) cc_final: 0.7971 (mtt90) outliers start: 8 outliers final: 8 residues processed: 49 average time/residue: 0.1303 time to fit residues: 7.8852 Evaluate side-chains 49 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 32 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.0870 chunk 39 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 47 optimal weight: 40.0000 chunk 28 optimal weight: 10.0000 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.163939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.112182 restraints weight = 7044.334| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 0.74 r_work: 0.2715 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7493 Z= 0.139 Angle : 0.499 5.924 10897 Z= 0.306 Chirality : 0.037 0.243 1324 Planarity : 0.004 0.032 771 Dihedral : 22.534 133.007 3013 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.61 % Allowed : 9.65 % Favored : 88.74 % 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: 1.12 (0.40), residues: 423 helix: 1.45 (0.35), residues: 214 sheet: 0.92 (0.63), residues: 64 loop : -0.31 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.012 0.001 TYR A 245 PHE 0.008 0.001 PHE A 47 TRP 0.009 0.001 TRP A 157 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 7493) covalent geometry : angle 0.49905 / 0.31 (10897) hydrogen bonds : bond 0.06223 / 3.78 ( 321) hydrogen bonds : angle 3.50125 / 2.50 ( 752) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.216 Fit side-chains REVERT: A 119 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: A 205 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.7965 (mtpp) REVERT: A 346 ARG cc_start: 0.8525 (mpt180) cc_final: 0.8292 (mmt-90) REVERT: A 352 ARG cc_start: 0.8532 (ttm-80) cc_final: 0.7990 (mtt90) outliers start: 6 outliers final: 4 residues processed: 47 average time/residue: 0.1456 time to fit residues: 8.4206 Evaluate side-chains 48 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 36 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.162279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.109748 restraints weight = 7088.672| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 0.79 r_work: 0.2682 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7493 Z= 0.187 Angle : 0.541 6.258 10897 Z= 0.323 Chirality : 0.039 0.243 1324 Planarity : 0.005 0.036 771 Dihedral : 22.515 134.505 3013 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.68 % Allowed : 9.12 % Favored : 88.20 % 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: 0.95 (0.40), residues: 423 helix: 1.33 (0.35), residues: 214 sheet: 0.89 (0.61), residues: 64 loop : -0.46 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 352 TYR 0.015 0.002 TYR A 245 PHE 0.010 0.002 PHE A 328 TRP 0.010 0.002 TRP A 157 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 ( 7493) covalent geometry : angle 0.54142 / 0.32 (10897) hydrogen bonds : bond 0.06698 / 4.08 ( 321) hydrogen bonds : angle 3.54684 / 2.52 ( 752) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.186 Fit side-chains REVERT: A 119 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: A 352 ARG cc_start: 0.8526 (ttm-80) cc_final: 0.7953 (mtt90) outliers start: 10 outliers final: 8 residues processed: 48 average time/residue: 0.1316 time to fit residues: 7.8005 Evaluate side-chains 51 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 30 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.162709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.111126 restraints weight = 7081.194| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 0.74 r_work: 0.2702 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7493 Z= 0.189 Angle : 0.535 5.706 10897 Z= 0.320 Chirality : 0.039 0.242 1324 Planarity : 0.005 0.038 771 Dihedral : 22.497 134.998 3013 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.41 % Allowed : 9.65 % Favored : 87.94 % 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: 0.91 (0.40), residues: 423 helix: 1.36 (0.35), residues: 213 sheet: 0.82 (0.63), residues: 63 loop : -0.55 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 123 TYR 0.014 0.002 TYR A 245 PHE 0.010 0.002 PHE A 328 TRP 0.010 0.002 TRP A 157 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 ( 7493) covalent geometry : angle 0.53503 / 0.32 (10897) hydrogen bonds : bond 0.06608 / 4.01 ( 321) hydrogen bonds : angle 3.54706 / 2.52 ( 752) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.168 Fit side-chains REVERT: A 119 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: A 352 ARG cc_start: 0.8502 (ttm-80) cc_final: 0.7936 (mtt90) outliers start: 9 outliers final: 7 residues processed: 50 average time/residue: 0.1354 time to fit residues: 8.3366 Evaluate side-chains 49 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 43 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 53 optimal weight: 30.0000 chunk 47 optimal weight: 40.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.168091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.116790 restraints weight = 7079.135| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 0.72 r_work: 0.2711 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7493 Z= 0.113 Angle : 0.471 5.618 10897 Z= 0.293 Chirality : 0.036 0.231 1324 Planarity : 0.004 0.036 771 Dihedral : 22.434 134.325 3013 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.34 % Allowed : 11.26 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.40), residues: 423 helix: 1.73 (0.36), residues: 212 sheet: 1.05 (0.63), residues: 64 loop : -0.48 (0.47), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 306 TYR 0.011 0.001 TYR A 245 PHE 0.009 0.001 PHE A 52 TRP 0.007 0.001 TRP A 157 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 ( 7493) covalent geometry : angle 0.47062 / 0.29 (10897) hydrogen bonds : bond 0.05886 / 3.53 ( 321) hydrogen bonds : angle 3.42585 / 2.45 ( 752) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.181 Fit side-chains REVERT: A 119 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: A 259 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7668 (mt-10) REVERT: A 352 ARG cc_start: 0.8542 (ttm-80) cc_final: 0.8064 (mtt180) outliers start: 5 outliers final: 3 residues processed: 47 average time/residue: 0.1307 time to fit residues: 7.5854 Evaluate side-chains 46 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 37 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 0.0060 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 0.0770 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.169853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.116750 restraints weight = 7012.517| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 0.77 r_work: 0.2718 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7493 Z= 0.100 Angle : 0.461 5.286 10897 Z= 0.289 Chirality : 0.035 0.235 1324 Planarity : 0.004 0.037 771 Dihedral : 22.410 133.628 3013 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.07 % Allowed : 11.80 % Favored : 87.13 % 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: 1.58 (0.41), residues: 423 helix: 2.01 (0.37), residues: 212 sheet: 1.23 (0.64), residues: 64 loop : -0.46 (0.47), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 254 TYR 0.009 0.001 TYR A 86 PHE 0.011 0.001 PHE A 52 TRP 0.003 0.001 TRP A 157 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00174 / 0.10 ( 7493) covalent geometry : angle 0.46140 / 0.29 (10897) hydrogen bonds : bond 0.05611 / 3.36 ( 321) hydrogen bonds : angle 3.37837 / 2.43 ( 752) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.174 Fit side-chains REVERT: A 119 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: A 259 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7681 (mt-10) REVERT: A 352 ARG cc_start: 0.8563 (ttm-80) cc_final: 0.8104 (mtt180) outliers start: 4 outliers final: 2 residues processed: 45 average time/residue: 0.1401 time to fit residues: 7.7280 Evaluate side-chains 45 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 50.0000 chunk 36 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.162554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.110815 restraints weight = 7102.514| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 0.75 r_work: 0.2692 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7493 Z= 0.185 Angle : 0.526 5.682 10897 Z= 0.314 Chirality : 0.039 0.236 1324 Planarity : 0.005 0.037 771 Dihedral : 22.396 134.941 3013 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.61 % Allowed : 10.99 % Favored : 87.40 % 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: 1.15 (0.40), residues: 423 helix: 1.56 (0.36), residues: 214 sheet: 0.99 (0.64), residues: 63 loop : -0.48 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 123 TYR 0.013 0.002 TYR A 245 PHE 0.011 0.002 PHE A 47 TRP 0.007 0.001 TRP A 157 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 7493) covalent geometry : angle 0.52559 / 0.31 (10897) hydrogen bonds : bond 0.06514 / 3.95 ( 321) hydrogen bonds : angle 3.47425 / 2.48 ( 752) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.179 Fit side-chains REVERT: A 119 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: A 259 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 352 ARG cc_start: 0.8543 (ttm-80) cc_final: 0.7982 (mtt90) outliers start: 6 outliers final: 3 residues processed: 44 average time/residue: 0.1334 time to fit residues: 7.1884 Evaluate side-chains 45 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 345 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 56 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 48 optimal weight: 50.0000 chunk 16 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.162753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.112365 restraints weight = 7043.840| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 0.76 r_work: 0.2702 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7493 Z= 0.165 Angle : 0.515 5.526 10897 Z= 0.309 Chirality : 0.037 0.236 1324 Planarity : 0.005 0.038 771 Dihedral : 22.400 135.010 3013 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.61 % Allowed : 11.26 % Favored : 87.13 % 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: 1.10 (0.40), residues: 423 helix: 1.51 (0.36), residues: 214 sheet: 0.99 (0.64), residues: 63 loop : -0.49 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 123 TYR 0.014 0.002 TYR A 245 PHE 0.009 0.002 PHE A 47 TRP 0.007 0.001 TRP A 157 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 7493) covalent geometry : angle 0.51520 / 0.31 (10897) hydrogen bonds : bond 0.06419 / 3.89 ( 321) hydrogen bonds : angle 3.47492 / 2.48 ( 752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1578.19 seconds wall clock time: 27 minutes 50.01 seconds (1670.01 seconds total)