Starting phenix.real_space_refine on Wed Sep 17 03:19:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xo9_38523/09_2025/8xo9_38523.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xo9_38523/09_2025/8xo9_38523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xo9_38523/09_2025/8xo9_38523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xo9_38523/09_2025/8xo9_38523.map" model { file = "/net/cci-nas-00/data/ceres_data/8xo9_38523/09_2025/8xo9_38523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xo9_38523/09_2025/8xo9_38523.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.057 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 27 5.16 5 C 1937 2.51 5 N 454 2.21 5 O 490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2908 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2896 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'E5E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.01, per 1000 atoms: 0.35 Number of scatterers: 2908 At special positions: 0 Unit cell: (54.4, 71.4, 75.65, 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 27 16.00 O 490 8.00 N 454 7.00 C 1937 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: 0.32 Conformation dependent library (CDL) restraints added in 122.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 708 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 91.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 19 through 54 removed outlier: 4.147A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 124 through 157 removed outlier: 3.881A pdb=" N LEU A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.894A pdb=" N GLY A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 151 " --> pdb=" O PRO A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 178 removed outlier: 3.640A pdb=" N PHE A 166 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 211 removed outlier: 3.657A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.737A pdb=" N ASN A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 222 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 249 through 269 Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 291 through 312 removed outlier: 4.157A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 323 Processing helix chain 'A' and resid 328 through 333 removed outlier: 4.149A pdb=" N VAL A 332 " --> pdb=" O TRP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 4.052A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 380 through 383 Processing helix chain 'A' and resid 384 through 414 removed outlier: 3.604A pdb=" N ASN A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 417 through 447 removed outlier: 4.342A pdb=" N VAL A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 448 through 464 removed outlier: 3.610A pdb=" N LEU A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 removed outlier: 3.734A pdb=" N PHE A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) 244 hydrogen bonds defined for protein. 723 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: 0.44 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 870 1.34 - 1.46: 645 1.46 - 1.58: 1416 1.58 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 2977 Sorted by residual: bond pdb=" CAJ E5E A 601 " pdb=" OAC E5E A 601 " ideal model delta sigma weight residual 1.350 1.401 -0.051 2.00e-02 2.50e+03 6.57e+00 bond pdb=" N MET A 175 " pdb=" CA MET A 175 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.19e+00 bond pdb=" N MET A 431 " pdb=" CA MET A 431 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.83e+00 bond pdb=" N PHE A 176 " pdb=" CA PHE A 176 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.76e+00 bond pdb=" CAI E5E A 601 " pdb=" OAB E5E A 601 " ideal model delta sigma weight residual 1.354 1.401 -0.047 2.00e-02 2.50e+03 5.45e+00 ... (remaining 2972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 3952 1.93 - 3.86: 73 3.86 - 5.80: 21 5.80 - 7.73: 5 7.73 - 9.66: 2 Bond angle restraints: 4053 Sorted by residual: angle pdb=" C ALA A 177 " pdb=" N PHE A 178 " pdb=" CA PHE A 178 " ideal model delta sigma weight residual 122.86 116.34 6.52 1.53e+00 4.27e-01 1.81e+01 angle pdb=" CA MET A 175 " pdb=" C MET A 175 " pdb=" O MET A 175 " ideal model delta sigma weight residual 120.82 117.57 3.25 1.05e+00 9.07e-01 9.60e+00 angle pdb=" C ASP A 123 " pdb=" N LEU A 124 " pdb=" CA LEU A 124 " ideal model delta sigma weight residual 121.54 127.10 -5.56 1.91e+00 2.74e-01 8.47e+00 angle pdb=" CA ILE A 447 " pdb=" C ILE A 447 " pdb=" N GLY A 448 " ideal model delta sigma weight residual 116.60 120.72 -4.12 1.45e+00 4.76e-01 8.09e+00 angle pdb=" CA PHE A 176 " pdb=" CB PHE A 176 " pdb=" CG PHE A 176 " ideal model delta sigma weight residual 113.80 116.62 -2.82 1.00e+00 1.00e+00 7.97e+00 ... (remaining 4048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 1539 17.52 - 35.04: 165 35.04 - 52.57: 37 52.57 - 70.09: 2 70.09 - 87.61: 1 Dihedral angle restraints: 1744 sinusoidal: 634 harmonic: 1110 Sorted by residual: dihedral pdb=" CA LEU A 270 " pdb=" C LEU A 270 " pdb=" N GLN A 271 " pdb=" CA GLN A 271 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CB GLU A 127 " pdb=" CG GLU A 127 " pdb=" CD GLU A 127 " pdb=" OE1 GLU A 127 " ideal model delta sinusoidal sigma weight residual 0.00 -87.61 87.61 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA PRO A 42 " pdb=" C PRO A 42 " pdb=" N ILE A 43 " pdb=" CA ILE A 43 " ideal model delta harmonic sigma weight residual -180.00 -164.09 -15.91 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 1741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 360 0.044 - 0.088: 104 0.088 - 0.132: 22 0.132 - 0.177: 1 0.177 - 0.221: 2 Chirality restraints: 489 Sorted by residual: chirality pdb=" CA PHE A 176 " pdb=" N PHE A 176 " pdb=" C PHE A 176 " pdb=" CB PHE A 176 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CAL E5E A 601 " pdb=" CAH E5E A 601 " pdb=" CAK E5E A 601 " pdb=" OAD E5E A 601 " both_signs ideal model delta sigma weight residual False -2.31 -2.51 0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CA PHE A 348 " pdb=" N PHE A 348 " pdb=" C PHE A 348 " pdb=" CB PHE A 348 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 486 not shown) Planarity restraints: 496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 124 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C LEU A 124 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU A 124 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU A 125 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 235 " 0.042 5.00e-02 4.00e+02 6.25e-02 6.26e+00 pdb=" N PRO A 236 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 236 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 236 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 473 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO A 474 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 474 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 474 " 0.031 5.00e-02 4.00e+02 ... (remaining 493 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 747 2.81 - 3.33: 2964 3.33 - 3.85: 4782 3.85 - 4.38: 4949 4.38 - 4.90: 9157 Nonbonded interactions: 22599 Sorted by model distance: nonbonded pdb=" OG SER A 325 " pdb=" OE1 GLN A 329 " model vdw 2.284 3.040 nonbonded pdb=" OD2 ASP A 33 " pdb=" OG SER A 196 " model vdw 2.519 3.040 nonbonded pdb=" OG SER A 181 " pdb=" N TYR A 182 " model vdw 2.545 3.120 nonbonded pdb=" O ALA A 333 " pdb=" ND2 ASN A 388 " model vdw 2.568 3.120 nonbonded pdb=" O PRO A 473 " pdb=" CA PRO A 474 " model vdw 2.582 2.776 ... (remaining 22594 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: 2.190 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.250 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 0.004 0.051 2977 Z= 0.206 Angle : 0.739 9.662 4053 Z= 0.391 Chirality : 0.043 0.221 489 Planarity : 0.006 0.063 496 Dihedral : 14.590 87.612 1036 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 21.12 % Favored : 78.88 % 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 aren not related in a simple way. whole: 1.96 (0.44), residues: 388 helix: 1.80 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -1.67 (0.75), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 155 TYR 0.013 0.001 TYR A 49 PHE 0.019 0.002 PHE A 468 TRP 0.011 0.002 TRP A 318 HIS 0.006 0.002 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 2977) covalent geometry : angle 0.73901 ( 4053) hydrogen bonds : bond 0.13416 ( 244) hydrogen bonds : angle 5.25298 ( 723) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.106 Fit side-chains REVERT: A 225 LEU cc_start: 0.7535 (mm) cc_final: 0.6771 (tt) REVERT: A 244 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8344 (tm-30) REVERT: A 405 ILE cc_start: 0.8787 (mm) cc_final: 0.8555 (mt) REVERT: A 431 MET cc_start: 0.8307 (mmt) cc_final: 0.8028 (mmt) REVERT: A 459 ILE cc_start: 0.7168 (mt) cc_final: 0.6903 (mm) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0544 time to fit residues: 3.1634 Evaluate side-chains 44 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 192 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.162669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133713 restraints weight = 3773.536| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.36 r_work: 0.3481 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2977 Z= 0.152 Angle : 0.665 9.542 4053 Z= 0.323 Chirality : 0.041 0.147 489 Planarity : 0.006 0.054 496 Dihedral : 5.591 35.696 416 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.65 % Allowed : 21.12 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.45), residues: 388 helix: 2.10 (0.30), residues: 328 sheet: None (None), residues: 0 loop : -2.19 (0.72), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 155 TYR 0.009 0.001 TYR A 49 PHE 0.016 0.002 PHE A 27 TRP 0.009 0.001 TRP A 328 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 2977) covalent geometry : angle 0.66502 ( 4053) hydrogen bonds : bond 0.05431 ( 244) hydrogen bonds : angle 4.29593 ( 723) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.102 Fit side-chains REVERT: A 225 LEU cc_start: 0.7106 (mm) cc_final: 0.6210 (tt) REVERT: A 405 ILE cc_start: 0.8304 (mm) cc_final: 0.8040 (mt) REVERT: A 459 ILE cc_start: 0.6311 (mt) cc_final: 0.6041 (mm) outliers start: 5 outliers final: 3 residues processed: 49 average time/residue: 0.0486 time to fit residues: 3.1006 Evaluate side-chains 45 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 0.8980 chunk 15 optimal weight: 0.0470 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.162692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.133892 restraints weight = 3742.160| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.34 r_work: 0.3487 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2977 Z= 0.141 Angle : 0.648 9.585 4053 Z= 0.311 Chirality : 0.040 0.137 489 Planarity : 0.006 0.051 496 Dihedral : 4.907 23.482 416 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.63 % Allowed : 18.48 % Favored : 77.89 % 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 aren not related in a simple way. whole: 2.50 (0.45), residues: 388 helix: 2.26 (0.30), residues: 326 sheet: None (None), residues: 0 loop : -1.79 (0.73), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 155 TYR 0.009 0.001 TYR A 49 PHE 0.014 0.001 PHE A 27 TRP 0.008 0.001 TRP A 328 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 2977) covalent geometry : angle 0.64801 ( 4053) hydrogen bonds : bond 0.05088 ( 244) hydrogen bonds : angle 4.14932 ( 723) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.111 Fit side-chains REVERT: A 196 SER cc_start: 0.7794 (t) cc_final: 0.7396 (p) REVERT: A 225 LEU cc_start: 0.7057 (mm) cc_final: 0.6142 (tt) REVERT: A 459 ILE cc_start: 0.6308 (OUTLIER) cc_final: 0.6023 (mm) outliers start: 11 outliers final: 6 residues processed: 52 average time/residue: 0.0509 time to fit residues: 3.4695 Evaluate side-chains 48 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.2980 chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.0870 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.163343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.134634 restraints weight = 3701.465| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.33 r_work: 0.3492 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2977 Z= 0.135 Angle : 0.644 9.573 4053 Z= 0.306 Chirality : 0.040 0.138 489 Planarity : 0.006 0.051 496 Dihedral : 4.573 17.984 416 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.31 % Allowed : 21.78 % Favored : 75.91 % 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 aren not related in a simple way. whole: 2.62 (0.45), residues: 388 helix: 2.35 (0.30), residues: 326 sheet: None (None), residues: 0 loop : -1.82 (0.73), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 155 TYR 0.008 0.001 TYR A 49 PHE 0.014 0.001 PHE A 27 TRP 0.008 0.001 TRP A 328 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 2977) covalent geometry : angle 0.64423 ( 4053) hydrogen bonds : bond 0.04813 ( 244) hydrogen bonds : angle 4.04452 ( 723) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.116 Fit side-chains REVERT: A 196 SER cc_start: 0.7841 (t) cc_final: 0.7417 (p) REVERT: A 225 LEU cc_start: 0.6985 (mm) cc_final: 0.6044 (tt) REVERT: A 459 ILE cc_start: 0.6300 (mt) cc_final: 0.6003 (mm) outliers start: 7 outliers final: 6 residues processed: 51 average time/residue: 0.0477 time to fit residues: 3.1806 Evaluate side-chains 49 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 338 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 4 optimal weight: 0.0040 chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.159951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.131523 restraints weight = 3693.636| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.21 r_work: 0.3454 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2977 Z= 0.154 Angle : 0.658 9.496 4053 Z= 0.317 Chirality : 0.041 0.140 489 Planarity : 0.006 0.055 496 Dihedral : 4.532 18.455 416 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.63 % Allowed : 20.46 % Favored : 75.91 % 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 aren not related in a simple way. whole: 2.57 (0.45), residues: 388 helix: 2.32 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -1.73 (0.73), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 155 TYR 0.010 0.001 TYR A 49 PHE 0.014 0.002 PHE A 27 TRP 0.008 0.001 TRP A 318 HIS 0.004 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 2977) covalent geometry : angle 0.65846 ( 4053) hydrogen bonds : bond 0.05384 ( 244) hydrogen bonds : angle 4.07936 ( 723) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.108 Fit side-chains REVERT: A 196 SER cc_start: 0.7968 (t) cc_final: 0.7562 (p) REVERT: A 225 LEU cc_start: 0.7198 (mm) cc_final: 0.6231 (tt) REVERT: A 405 ILE cc_start: 0.8562 (mm) cc_final: 0.8298 (mt) outliers start: 11 outliers final: 7 residues processed: 52 average time/residue: 0.0458 time to fit residues: 3.1709 Evaluate side-chains 51 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.159979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.131361 restraints weight = 3751.466| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.23 r_work: 0.3451 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2977 Z= 0.149 Angle : 0.657 9.503 4053 Z= 0.317 Chirality : 0.041 0.137 489 Planarity : 0.006 0.059 496 Dihedral : 4.498 17.924 416 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.63 % Allowed : 20.79 % Favored : 75.58 % 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 aren not related in a simple way. whole: 2.60 (0.45), residues: 388 helix: 2.33 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -1.73 (0.75), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 155 TYR 0.012 0.001 TYR A 49 PHE 0.015 0.001 PHE A 27 TRP 0.008 0.001 TRP A 318 HIS 0.004 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 2977) covalent geometry : angle 0.65736 ( 4053) hydrogen bonds : bond 0.05292 ( 244) hydrogen bonds : angle 4.03013 ( 723) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.107 Fit side-chains REVERT: A 196 SER cc_start: 0.7963 (t) cc_final: 0.7557 (p) REVERT: A 225 LEU cc_start: 0.7088 (mm) cc_final: 0.6101 (tt) REVERT: A 405 ILE cc_start: 0.8572 (mm) cc_final: 0.8309 (mt) REVERT: A 459 ILE cc_start: 0.6634 (OUTLIER) cc_final: 0.6325 (mm) outliers start: 11 outliers final: 7 residues processed: 53 average time/residue: 0.0531 time to fit residues: 3.6046 Evaluate side-chains 51 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.0670 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.161492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132970 restraints weight = 3747.768| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.23 r_work: 0.3472 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2977 Z= 0.138 Angle : 0.646 9.482 4053 Z= 0.311 Chirality : 0.040 0.133 489 Planarity : 0.006 0.056 496 Dihedral : 4.392 18.475 416 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.29 % Allowed : 21.45 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.71 (0.45), residues: 388 helix: 2.44 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -1.90 (0.71), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 357 TYR 0.010 0.001 TYR A 49 PHE 0.014 0.001 PHE A 27 TRP 0.008 0.001 TRP A 328 HIS 0.001 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 2977) covalent geometry : angle 0.64629 ( 4053) hydrogen bonds : bond 0.04865 ( 244) hydrogen bonds : angle 3.94603 ( 723) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.107 Fit side-chains REVERT: A 196 SER cc_start: 0.7902 (t) cc_final: 0.7511 (p) REVERT: A 225 LEU cc_start: 0.7038 (mm) cc_final: 0.6106 (tt) REVERT: A 397 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6985 (mtm) REVERT: A 405 ILE cc_start: 0.8527 (mm) cc_final: 0.8251 (mt) REVERT: A 459 ILE cc_start: 0.6635 (mt) cc_final: 0.6326 (mm) outliers start: 13 outliers final: 6 residues processed: 58 average time/residue: 0.0511 time to fit residues: 3.8008 Evaluate side-chains 53 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 397 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 0.0970 chunk 8 optimal weight: 0.5980 chunk 21 optimal weight: 0.0370 chunk 19 optimal weight: 0.0970 chunk 14 optimal weight: 0.9980 overall best weight: 0.1854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.167545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.139090 restraints weight = 3720.219| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.26 r_work: 0.3526 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2977 Z= 0.124 Angle : 0.651 10.110 4053 Z= 0.306 Chirality : 0.040 0.124 489 Planarity : 0.006 0.048 496 Dihedral : 4.223 17.764 416 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.30 % Allowed : 22.11 % Favored : 74.59 % 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 aren not related in a simple way. whole: 2.99 (0.45), residues: 388 helix: 2.66 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -1.74 (0.70), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 274 TYR 0.009 0.001 TYR A 49 PHE 0.013 0.001 PHE A 27 TRP 0.010 0.001 TRP A 328 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 2977) covalent geometry : angle 0.65128 ( 4053) hydrogen bonds : bond 0.03990 ( 244) hydrogen bonds : angle 3.81013 ( 723) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.107 Fit side-chains REVERT: A 225 LEU cc_start: 0.6915 (mm) cc_final: 0.6047 (tt) REVERT: A 459 ILE cc_start: 0.6547 (mt) cc_final: 0.6250 (mm) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 0.0531 time to fit residues: 4.1437 Evaluate side-chains 52 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 415 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 0.0570 chunk 16 optimal weight: 0.0070 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 chunk 38 optimal weight: 0.0570 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 overall best weight: 0.1834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 53 HIS A 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.167381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.139073 restraints weight = 3784.928| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.29 r_work: 0.3535 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2977 Z= 0.124 Angle : 0.660 10.612 4053 Z= 0.309 Chirality : 0.040 0.122 489 Planarity : 0.005 0.045 496 Dihedral : 4.124 17.968 416 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.64 % Allowed : 23.76 % Favored : 73.60 % 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 aren not related in a simple way. whole: 3.03 (0.45), residues: 388 helix: 2.65 (0.30), residues: 323 sheet: None (None), residues: 0 loop : -1.53 (0.71), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 155 TYR 0.009 0.001 TYR A 49 PHE 0.013 0.001 PHE A 27 TRP 0.009 0.001 TRP A 328 HIS 0.001 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 2977) covalent geometry : angle 0.66041 ( 4053) hydrogen bonds : bond 0.04011 ( 244) hydrogen bonds : angle 3.77316 ( 723) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.113 Fit side-chains REVERT: A 225 LEU cc_start: 0.6821 (mm) cc_final: 0.5990 (tt) REVERT: A 351 LEU cc_start: 0.4960 (OUTLIER) cc_final: 0.4741 (mp) REVERT: A 397 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.6960 (mtm) outliers start: 8 outliers final: 6 residues processed: 57 average time/residue: 0.0517 time to fit residues: 3.7582 Evaluate side-chains 56 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 415 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.161308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133076 restraints weight = 3780.237| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.26 r_work: 0.3471 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2977 Z= 0.148 Angle : 0.698 10.604 4053 Z= 0.328 Chirality : 0.041 0.131 489 Planarity : 0.006 0.055 496 Dihedral : 4.161 17.495 416 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.64 % Allowed : 23.76 % Favored : 73.60 % 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 aren not related in a simple way. whole: 2.69 (0.45), residues: 388 helix: 2.35 (0.30), residues: 328 sheet: None (None), residues: 0 loop : -1.63 (0.75), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 155 TYR 0.012 0.001 TYR A 49 PHE 0.013 0.001 PHE A 348 TRP 0.006 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 2977) covalent geometry : angle 0.69785 ( 4053) hydrogen bonds : bond 0.05035 ( 244) hydrogen bonds : angle 3.90767 ( 723) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 776 Ramachandran restraints generated. 388 Oldfield, 0 Emsley, 388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.100 Fit side-chains REVERT: A 225 LEU cc_start: 0.6822 (mm) cc_final: 0.5939 (tt) REVERT: A 397 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6994 (mtm) outliers start: 8 outliers final: 6 residues processed: 52 average time/residue: 0.0452 time to fit residues: 3.0643 Evaluate side-chains 51 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 415 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 0.0040 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.163310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.135202 restraints weight = 3754.165| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.23 r_work: 0.3485 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2977 Z= 0.143 Angle : 0.673 10.718 4053 Z= 0.322 Chirality : 0.041 0.153 489 Planarity : 0.006 0.055 496 Dihedral : 4.262 18.077 416 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.64 % Allowed : 23.76 % Favored : 73.60 % 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 aren not related in a simple way. whole: 2.67 (0.45), residues: 388 helix: 2.34 (0.30), residues: 327 sheet: None (None), residues: 0 loop : -1.61 (0.74), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 155 TYR 0.012 0.001 TYR A 49 PHE 0.012 0.001 PHE A 348 TRP 0.007 0.001 TRP A 328 HIS 0.001 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 2977) covalent geometry : angle 0.67339 ( 4053) hydrogen bonds : bond 0.04807 ( 244) hydrogen bonds : angle 3.90654 ( 723) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 833.05 seconds wall clock time: 14 minutes 57.58 seconds (897.58 seconds total)