Starting phenix.real_space_refine on Wed Jul 1 22:20:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gof_34177/07_2026/8gof_34177.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gof_34177/07_2026/8gof_34177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gof_34177/07_2026/8gof_34177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gof_34177/07_2026/8gof_34177.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gof_34177/07_2026/8gof_34177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gof_34177/07_2026/8gof_34177.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8gof_34177/07_2026/8gof_34177.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gof_34177/07_2026/8gof_34177.cif" } resolution = 3.0 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 2192 2.51 5 N 545 2.21 5 O 552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 3299 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3268 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 14, 'TRANS': 392} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'LYA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.01, per 1000 atoms: 0.31 Number of scatterers: 3299 At special positions: 0 Unit cell: (80, 72, 66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 552 8.00 N 545 7.00 C 2192 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: 0.31 Conformation dependent library (CDL) restraints added in 125.5 milliseconds 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 83.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 25 through 39 removed outlier: 3.520A pdb=" N CYS A 30 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR A 31 " --> pdb=" O HIS A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 60 through 68 removed outlier: 3.517A pdb=" N ASN A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 79 removed outlier: 3.716A pdb=" N TYR A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 removed outlier: 4.241A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 113 removed outlier: 3.524A pdb=" N PHE A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.517A pdb=" N THR A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 removed outlier: 4.402A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 176 removed outlier: 3.667A pdb=" N VAL A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 202 removed outlier: 3.827A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.886A pdb=" N ASP A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 278 through 296 removed outlier: 3.558A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 305 through 324 removed outlier: 3.698A pdb=" N THR A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 329 through 333 removed outlier: 3.889A pdb=" N ALA A 332 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG A 333 " --> pdb=" O ARG A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 333' Processing helix chain 'A' and resid 335 through 355 removed outlier: 3.549A pdb=" N THR A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 388 removed outlier: 3.534A pdb=" N PHE A 369 " --> pdb=" O CYS A 365 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 392 through 418 removed outlier: 3.520A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 453 removed outlier: 3.504A pdb=" N GLN A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 654 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.50 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 987 1.34 - 1.46: 765 1.46 - 1.57: 1623 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 3391 Sorted by residual: bond pdb=" N MET A 130 " pdb=" CA MET A 130 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.04e+00 bond pdb=" C12 LYA A 601 " pdb=" N11 LYA A 601 " ideal model delta sigma weight residual 1.340 1.370 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C10 LYA A 601 " pdb=" N11 LYA A 601 " ideal model delta sigma weight residual 1.384 1.355 0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C VAL A 81 " pdb=" O VAL A 81 " ideal model delta sigma weight residual 1.240 1.223 0.017 1.26e-02 6.30e+03 1.82e+00 bond pdb=" C17 LYA A 601 " pdb=" N16 LYA A 601 " ideal model delta sigma weight residual 1.305 1.331 -0.026 2.00e-02 2.50e+03 1.72e+00 ... (remaining 3386 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 4424 1.62 - 3.24: 153 3.24 - 4.86: 32 4.86 - 6.48: 8 6.48 - 8.10: 5 Bond angle restraints: 4622 Sorted by residual: angle pdb=" N PHE A 103 " pdb=" CA PHE A 103 " pdb=" C PHE A 103 " ideal model delta sigma weight residual 111.40 105.48 5.92 1.22e+00 6.72e-01 2.35e+01 angle pdb=" C TYR A 92 " pdb=" CA TYR A 92 " pdb=" CB TYR A 92 " ideal model delta sigma weight residual 110.42 102.32 8.10 1.99e+00 2.53e-01 1.66e+01 angle pdb=" N LEU A 162 " pdb=" CA LEU A 162 " pdb=" C LEU A 162 " ideal model delta sigma weight residual 112.23 107.69 4.54 1.26e+00 6.30e-01 1.30e+01 angle pdb=" N ILE A 329 " pdb=" CA ILE A 329 " pdb=" C ILE A 329 " ideal model delta sigma weight residual 112.96 109.62 3.34 1.00e+00 1.00e+00 1.12e+01 angle pdb=" N VAL A 428 " pdb=" CA VAL A 428 " pdb=" C VAL A 428 " ideal model delta sigma weight residual 111.17 115.69 -4.52 1.38e+00 5.25e-01 1.07e+01 ... (remaining 4617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.09: 1753 15.09 - 30.17: 144 30.17 - 45.25: 27 45.25 - 60.34: 13 60.34 - 75.42: 3 Dihedral angle restraints: 1940 sinusoidal: 742 harmonic: 1198 Sorted by residual: dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 154.19 25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CB ARG A 373 " pdb=" CG ARG A 373 " pdb=" CD ARG A 373 " pdb=" NE ARG A 373 " ideal model delta sinusoidal sigma weight residual 60.00 118.74 -58.74 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA VAL A 418 " pdb=" C VAL A 418 " pdb=" N SER A 419 " pdb=" CA SER A 419 " ideal model delta harmonic sigma weight residual 180.00 -164.62 -15.38 0 5.00e+00 4.00e-02 9.46e+00 ... (remaining 1937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 343 0.041 - 0.081: 157 0.081 - 0.122: 26 0.122 - 0.163: 7 0.163 - 0.203: 1 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA ARG A 42 " pdb=" N ARG A 42 " pdb=" C ARG A 42 " pdb=" CB ARG A 42 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB VAL A 288 " pdb=" CA VAL A 288 " pdb=" CG1 VAL A 288 " pdb=" CG2 VAL A 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA LYS A 57 " pdb=" N LYS A 57 " pdb=" C LYS A 57 " pdb=" CB LYS A 57 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 531 not shown) Planarity restraints: 559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 LYA A 601 " -0.041 2.00e-02 2.50e+03 1.04e-01 1.36e+02 pdb=" C23 LYA A 601 " 0.127 2.00e-02 2.50e+03 pdb=" C4 LYA A 601 " 0.097 2.00e-02 2.50e+03 pdb=" N22 LYA A 601 " -0.163 2.00e-02 2.50e+03 pdb=" O21 LYA A 601 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 69 " 0.044 5.00e-02 4.00e+02 6.50e-02 6.75e+00 pdb=" N PRO A 70 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 41 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C ILE A 41 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE A 41 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG A 42 " 0.013 2.00e-02 2.50e+03 ... (remaining 556 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 986 2.79 - 3.32: 2929 3.32 - 3.85: 5651 3.85 - 4.37: 7087 4.37 - 4.90: 11655 Nonbonded interactions: 28308 Sorted by model distance: nonbonded pdb=" O VAL A 83 " pdb=" OG1 THR A 87 " model vdw 2.269 3.040 nonbonded pdb=" OD1 ASP A 88 " pdb=" OH TYR A 92 " model vdw 2.271 3.040 nonbonded pdb=" O VAL A 304 " pdb=" OH TYR A 366 " model vdw 2.278 3.040 nonbonded pdb=" O LEU A 32 " pdb=" OH TYR A 136 " model vdw 2.298 3.040 nonbonded pdb=" O VAL A 380 " pdb=" OG1 THR A 384 " model vdw 2.324 3.040 ... (remaining 28303 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.350 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.300 Find NCS groups from input model: 0.010 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:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 0.056 3391 Z= 0.272 Angle : 0.799 8.103 4622 Z= 0.453 Chirality : 0.046 0.203 534 Planarity : 0.007 0.104 559 Dihedral : 12.708 75.420 1170 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % 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: -6.52 (0.22), residues: 403 helix: -4.45 (0.11), residues: 322 sheet: None (None), residues: 0 loop : -2.16 (0.54), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 133 TYR 0.011 0.002 TYR A 92 PHE 0.016 0.002 PHE A 37 TRP 0.010 0.002 TRP A 107 HIS 0.002 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.27 ( 3391) covalent geometry : angle 0.79892 / 0.45 ( 4622) hydrogen bonds : bond 0.27801 / 18.06 ( 220) hydrogen bonds : angle 11.32589 / 7.53 ( 654) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.121 Fit side-chains REVERT: A 60 THR cc_start: 0.8565 (m) cc_final: 0.8328 (p) REVERT: A 277 ASN cc_start: 0.8309 (t0) cc_final: 0.7975 (t160) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.6425 time to fit residues: 27.0574 Evaluate side-chains 29 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN A 293 ASN A 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.100139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.084242 restraints weight = 4230.094| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.63 r_work: 0.2777 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3391 Z= 0.163 Angle : 0.554 6.024 4622 Z= 0.295 Chirality : 0.039 0.131 534 Planarity : 0.005 0.040 559 Dihedral : 6.148 55.385 461 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.42 % Allowed : 11.11 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.34), residues: 403 helix: -1.66 (0.23), residues: 320 sheet: None (None), residues: 0 loop : -1.35 (0.61), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 303 TYR 0.013 0.001 TYR A 35 PHE 0.011 0.001 PHE A 372 TRP 0.015 0.001 TRP A 107 HIS 0.002 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 3391) covalent geometry : angle 0.55385 / 0.30 ( 4622) hydrogen bonds : bond 0.04249 / 2.82 ( 220) hydrogen bonds : angle 4.82035 / 3.28 ( 654) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.125 Fit side-chains REVERT: A 88 ASP cc_start: 0.8171 (m-30) cc_final: 0.7940 (m-30) REVERT: A 127 SER cc_start: 0.8852 (m) cc_final: 0.8568 (p) REVERT: A 204 LYS cc_start: 0.7905 (tttm) cc_final: 0.7506 (tttm) REVERT: A 251 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7402 (mm) outliers start: 5 outliers final: 0 residues processed: 41 average time/residue: 0.5783 time to fit residues: 24.4617 Evaluate side-chains 36 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.101079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.085399 restraints weight = 4111.221| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.57 r_work: 0.2792 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3391 Z= 0.143 Angle : 0.492 5.410 4622 Z= 0.260 Chirality : 0.038 0.126 534 Planarity : 0.004 0.032 559 Dihedral : 6.154 59.517 461 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.42 % Allowed : 12.82 % Favored : 85.75 % 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: -0.40 (0.39), residues: 403 helix: 0.06 (0.27), residues: 320 sheet: None (None), residues: 0 loop : -1.03 (0.61), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 303 TYR 0.012 0.001 TYR A 35 PHE 0.012 0.001 PHE A 372 TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 3391) covalent geometry : angle 0.49162 / 0.26 ( 4622) hydrogen bonds : bond 0.03718 / 2.49 ( 220) hydrogen bonds : angle 4.19892 / 2.87 ( 654) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.105 Fit side-chains REVERT: A 127 SER cc_start: 0.8833 (m) cc_final: 0.8583 (p) REVERT: A 204 LYS cc_start: 0.7875 (tttm) cc_final: 0.7456 (tttm) REVERT: A 251 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7219 (mm) REVERT: A 293 ASN cc_start: 0.8702 (t0) cc_final: 0.8325 (t0) outliers start: 5 outliers final: 0 residues processed: 36 average time/residue: 0.5571 time to fit residues: 20.6333 Evaluate side-chains 33 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.106188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.090083 restraints weight = 4072.325| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.64 r_work: 0.2822 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3391 Z= 0.138 Angle : 0.477 5.375 4622 Z= 0.250 Chirality : 0.038 0.127 534 Planarity : 0.003 0.029 559 Dihedral : 6.000 54.405 461 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.56 % Allowed : 13.39 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.41), residues: 403 helix: 0.85 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -0.95 (0.60), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 303 TYR 0.012 0.001 TYR A 35 PHE 0.011 0.001 PHE A 372 TRP 0.011 0.001 TRP A 107 HIS 0.001 0.000 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 3391) covalent geometry : angle 0.47681 / 0.25 ( 4622) hydrogen bonds : bond 0.03557 / 2.39 ( 220) hydrogen bonds : angle 3.98556 / 2.73 ( 654) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.122 Fit side-chains REVERT: A 162 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7494 (tt) REVERT: A 204 LYS cc_start: 0.7858 (tttm) cc_final: 0.7431 (tttm) REVERT: A 251 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7146 (mm) outliers start: 9 outliers final: 2 residues processed: 38 average time/residue: 0.5511 time to fit residues: 21.5880 Evaluate side-chains 35 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 277 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.103829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.087740 restraints weight = 4153.524| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.65 r_work: 0.2827 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3391 Z= 0.130 Angle : 0.470 5.343 4622 Z= 0.247 Chirality : 0.038 0.126 534 Planarity : 0.003 0.028 559 Dihedral : 5.868 49.392 461 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.28 % Allowed : 13.39 % Favored : 84.33 % 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: 1.08 (0.42), residues: 403 helix: 1.17 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -0.86 (0.60), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 303 TYR 0.011 0.001 TYR A 35 PHE 0.011 0.001 PHE A 372 TRP 0.011 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 3391) covalent geometry : angle 0.47031 / 0.25 ( 4622) hydrogen bonds : bond 0.03497 / 2.36 ( 220) hydrogen bonds : angle 3.88887 / 2.66 ( 654) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.103 Fit side-chains REVERT: A 162 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7459 (tt) REVERT: A 204 LYS cc_start: 0.7906 (tttm) cc_final: 0.7492 (tttm) REVERT: A 251 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7128 (mm) outliers start: 8 outliers final: 2 residues processed: 35 average time/residue: 0.5795 time to fit residues: 20.9073 Evaluate side-chains 33 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 251 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3131 r_free = 0.3131 target = 0.101436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.085472 restraints weight = 4145.863| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.64 r_work: 0.2792 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3391 Z= 0.174 Angle : 0.500 5.374 4622 Z= 0.261 Chirality : 0.040 0.134 534 Planarity : 0.003 0.030 559 Dihedral : 5.863 46.083 461 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.56 % Allowed : 13.39 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.42), residues: 403 helix: 1.26 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -0.81 (0.61), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 303 TYR 0.014 0.001 TYR A 35 PHE 0.010 0.001 PHE A 372 TRP 0.012 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 ( 3391) covalent geometry : angle 0.50042 / 0.26 ( 4622) hydrogen bonds : bond 0.03683 / 2.47 ( 220) hydrogen bonds : angle 3.97673 / 2.73 ( 654) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.085 Fit side-chains REVERT: A 162 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7528 (tt) REVERT: A 204 LYS cc_start: 0.7930 (tttm) cc_final: 0.7487 (tttm) REVERT: A 251 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7186 (mm) outliers start: 9 outliers final: 3 residues processed: 39 average time/residue: 0.5442 time to fit residues: 21.8625 Evaluate side-chains 34 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 251 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.086929 restraints weight = 4139.983| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.66 r_work: 0.2814 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3391 Z= 0.136 Angle : 0.473 5.336 4622 Z= 0.248 Chirality : 0.038 0.127 534 Planarity : 0.003 0.029 559 Dihedral : 5.631 40.777 461 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.99 % Allowed : 14.53 % Favored : 83.48 % 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: 1.41 (0.42), residues: 403 helix: 1.42 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.83 (0.62), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 303 TYR 0.011 0.001 TYR A 35 PHE 0.011 0.001 PHE A 372 TRP 0.012 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 3391) covalent geometry : angle 0.47317 / 0.25 ( 4622) hydrogen bonds : bond 0.03495 / 2.35 ( 220) hydrogen bonds : angle 3.85779 / 2.64 ( 654) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.080 Fit side-chains REVERT: A 162 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7517 (tt) REVERT: A 204 LYS cc_start: 0.8027 (tttm) cc_final: 0.7613 (tttm) REVERT: A 298 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8823 (t) REVERT: A 303 ARG cc_start: 0.8345 (ttp80) cc_final: 0.8056 (ttp80) outliers start: 7 outliers final: 3 residues processed: 37 average time/residue: 0.5709 time to fit residues: 21.6993 Evaluate side-chains 36 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 298 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 2 optimal weight: 0.0010 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.104163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.088120 restraints weight = 4170.476| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.66 r_work: 0.2837 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3391 Z= 0.119 Angle : 0.458 5.320 4622 Z= 0.240 Chirality : 0.037 0.123 534 Planarity : 0.003 0.028 559 Dihedral : 5.417 41.530 461 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.71 % Allowed : 15.38 % Favored : 82.91 % 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: 1.64 (0.42), residues: 403 helix: 1.59 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.80 (0.62), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 303 TYR 0.011 0.001 TYR A 92 PHE 0.011 0.001 PHE A 372 TRP 0.011 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 3391) covalent geometry : angle 0.45836 / 0.24 ( 4622) hydrogen bonds : bond 0.03346 / 2.26 ( 220) hydrogen bonds : angle 3.73781 / 2.56 ( 654) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.121 Fit side-chains REVERT: A 162 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7560 (tt) REVERT: A 298 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8843 (t) REVERT: A 303 ARG cc_start: 0.8314 (ttp80) cc_final: 0.8033 (ttp80) outliers start: 6 outliers final: 2 residues processed: 39 average time/residue: 0.6259 time to fit residues: 25.1258 Evaluate side-chains 34 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 298 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.0670 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3162 r_free = 0.3162 target = 0.103809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.088002 restraints weight = 4110.329| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.62 r_work: 0.2830 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3391 Z= 0.130 Angle : 0.469 5.330 4622 Z= 0.245 Chirality : 0.038 0.125 534 Planarity : 0.003 0.028 559 Dihedral : 5.600 40.646 461 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.42 % Allowed : 16.52 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.42), residues: 403 helix: 1.65 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.75 (0.62), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 303 TYR 0.011 0.001 TYR A 92 PHE 0.010 0.001 PHE A 372 TRP 0.012 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 3391) covalent geometry : angle 0.46900 / 0.24 ( 4622) hydrogen bonds : bond 0.03402 / 2.30 ( 220) hydrogen bonds : angle 3.74173 / 2.57 ( 654) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.124 Fit side-chains REVERT: A 162 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7455 (tt) REVERT: A 298 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8808 (t) REVERT: A 303 ARG cc_start: 0.8269 (ttp80) cc_final: 0.7966 (ttp80) outliers start: 5 outliers final: 2 residues processed: 34 average time/residue: 0.6794 time to fit residues: 23.7592 Evaluate side-chains 33 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 298 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.103982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.088013 restraints weight = 4070.696| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.63 r_work: 0.2833 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3391 Z= 0.126 Angle : 0.464 5.326 4622 Z= 0.242 Chirality : 0.038 0.124 534 Planarity : 0.003 0.028 559 Dihedral : 5.539 40.833 461 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.42 % Allowed : 16.24 % Favored : 82.34 % 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: 1.86 (0.42), residues: 403 helix: 1.73 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.69 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 303 TYR 0.010 0.001 TYR A 92 PHE 0.010 0.001 PHE A 372 TRP 0.011 0.001 TRP A 107 HIS 0.002 0.000 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 3391) covalent geometry : angle 0.46359 / 0.24 ( 4622) hydrogen bonds : bond 0.03372 / 2.28 ( 220) hydrogen bonds : angle 3.71630 / 2.55 ( 654) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.198 Fit side-chains REVERT: A 298 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8804 (t) REVERT: A 303 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7948 (ttp80) outliers start: 5 outliers final: 1 residues processed: 35 average time/residue: 0.6306 time to fit residues: 22.6702 Evaluate side-chains 30 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 298 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 0.0570 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.102794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.086863 restraints weight = 4139.534| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.65 r_work: 0.2810 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3391 Z= 0.151 Angle : 0.484 5.351 4622 Z= 0.251 Chirality : 0.039 0.130 534 Planarity : 0.003 0.029 559 Dihedral : 5.643 39.992 461 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.85 % Allowed : 16.81 % Favored : 82.34 % 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: 1.87 (0.42), residues: 403 helix: 1.73 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -0.66 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 303 TYR 0.011 0.001 TYR A 35 PHE 0.010 0.001 PHE A 372 TRP 0.012 0.001 TRP A 107 HIS 0.003 0.000 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 3391) covalent geometry : angle 0.48402 / 0.25 ( 4622) hydrogen bonds : bond 0.03515 / 2.37 ( 220) hydrogen bonds : angle 3.80344 / 2.62 ( 654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1159.94 seconds wall clock time: 20 minutes 31.09 seconds (1231.09 seconds total)