Starting phenix.real_space_refine on Thu Jul 2 17:39:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e40_27875/07_2026/8e40_27875.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e40_27875/07_2026/8e40_27875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8e40_27875/07_2026/8e40_27875.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e40_27875/07_2026/8e40_27875.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e40_27875/07_2026/8e40_27875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e40_27875/07_2026/8e40_27875.map" model { file = "/net/cci-nas-00/data/ceres_data/8e40_27875/07_2026/8e40_27875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e40_27875/07_2026/8e40_27875.cif" } resolution = 3.57 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3868 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 47 5.49 5 S 30 5.16 5 C 3835 2.51 5 N 1122 2.21 5 O 1261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s 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: 6297 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3085 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 347} Chain: "B" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1000 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1220 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 5, 'TRANS': 141} Chain: "R" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 456 Classifications: {'RNA': 22} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 14} Link IDs: {'rna3p': 21} Chain: "r" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 534 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 4, 'rna3p_pur': 13, 'rna3p_pyr': 8} Link IDs: {'rna2p': 3, 'rna3p': 21} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 757 SG CYS A 97 34.707 53.781 84.146 1.00 27.23 S ATOM 781 SG CYS A 100 30.843 53.501 86.010 1.00 32.88 S ATOM 2300 SG CYS A 287 59.635 23.728 72.488 1.00 60.84 S Time building chain proxies: 1.62, per 1000 atoms: 0.26 Number of scatterers: 6297 At special positions: 0 Unit cell: (92.92, 98.44, 134.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 30 16.00 P 47 15.00 O 1261 8.00 N 1122 7.00 C 3835 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: 0.49 Conformation dependent library (CDL) restraints added in 418.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 65 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 97 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 100 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 287 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 257 " 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1206 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 5 sheets defined 38.5% alpha, 16.7% beta 17 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 Processing helix chain 'A' and resid 65 through 79 Processing helix chain 'A' and resid 97 through 111 removed outlier: 4.056A pdb=" N THR A 106 " --> pdb=" O ASN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 142 removed outlier: 3.851A pdb=" N ALA A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 165 removed outlier: 3.825A pdb=" N VAL A 165 " --> pdb=" O TRP A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.962A pdb=" N THR A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 259 through 266 removed outlier: 3.890A pdb=" N LEU A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 270 Processing helix chain 'A' and resid 290 through 301 removed outlier: 3.758A pdb=" N MET A 294 " --> pdb=" O CYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 331 removed outlier: 4.049A pdb=" N GLY A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 362 through 379 Processing helix chain 'B' and resid 14 through 31 Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'C' and resid 6 through 13 Processing helix chain 'C' and resid 15 through 22 removed outlier: 3.866A pdb=" N ARG C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS C 20 " --> pdb=" O GLU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 50 Processing helix chain 'C' and resid 70 through 75 removed outlier: 4.295A pdb=" N GLN C 74 " --> pdb=" O PRO C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.916A pdb=" N GLU C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 149 removed outlier: 3.677A pdb=" N ARG C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 87 removed outlier: 6.767A pdb=" N TYR A 86 " --> pdb=" O THR A 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 234 through 240 removed outlier: 5.035A pdb=" N VAL A 224 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N GLN A 237 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 11.077A pdb=" N TYR A 222 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ARG A 277 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR A 276 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N CYS A 307 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL A 278 " --> pdb=" O CYS A 307 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE A 309 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS A 280 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA A 335 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE A 308 " --> pdb=" O ALA A 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 41 removed outlier: 6.492A pdb=" N THR B 68 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU B 54 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE B 66 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N HIS B 56 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU B 64 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 65 " --> pdb=" O GLU B 88 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY B 84 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ILE B 87 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE B 9 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N TRP B 89 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 14.398A pdb=" N VAL B 7 " --> pdb=" O TRP B 89 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 55 " --> pdb=" O PHE C 68 " (cutoff:3.500A) 204 hydrogen bonds defined for protein. 585 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.69 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: 1818 1.34 - 1.46: 1791 1.46 - 1.58: 2826 1.58 - 1.70: 92 1.70 - 1.82: 43 Bond restraints: 6570 Sorted by residual: bond pdb=" N LEU C 119 " pdb=" CA LEU C 119 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.18e+00 bond pdb=" N ASP C 34 " pdb=" CA ASP C 34 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.35e-02 5.49e+03 6.11e+00 bond pdb=" C VAL C 5 " pdb=" N PRO C 6 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.08e+00 bond pdb=" N ASP C 120 " pdb=" CA ASP C 120 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.82e+00 bond pdb=" N ARG C 118 " pdb=" CA ARG C 118 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.33e-02 5.65e+03 4.32e+00 ... (remaining 6565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 8712 2.02 - 4.05: 321 4.05 - 6.07: 56 6.07 - 8.09: 15 8.09 - 10.12: 7 Bond angle restraints: 9111 Sorted by residual: angle pdb=" CA LYS A 113 " pdb=" CB LYS A 113 " pdb=" CG LYS A 113 " ideal model delta sigma weight residual 114.10 124.22 -10.12 2.00e+00 2.50e-01 2.56e+01 angle pdb=" CA GLU C 38 " pdb=" CB GLU C 38 " pdb=" CG GLU C 38 " ideal model delta sigma weight residual 114.10 123.28 -9.18 2.00e+00 2.50e-01 2.11e+01 angle pdb=" CA GLU A 302 " pdb=" CB GLU A 302 " pdb=" CG GLU A 302 " ideal model delta sigma weight residual 114.10 123.07 -8.97 2.00e+00 2.50e-01 2.01e+01 angle pdb=" N LEU A 260 " pdb=" CA LEU A 260 " pdb=" C LEU A 260 " ideal model delta sigma weight residual 111.36 106.48 4.88 1.09e+00 8.42e-01 2.01e+01 angle pdb=" O3' U r 2 " pdb=" C3' U r 2 " pdb=" C2' U r 2 " ideal model delta sigma weight residual 113.70 120.40 -6.70 1.50e+00 4.44e-01 2.00e+01 ... (remaining 9106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.56: 3413 26.56 - 53.11: 327 53.11 - 79.67: 41 79.67 - 106.23: 4 106.23 - 132.79: 2 Dihedral angle restraints: 3787 sinusoidal: 1925 harmonic: 1862 Sorted by residual: dihedral pdb=" CA LYS B 161 " pdb=" C LYS B 161 " pdb=" N PRO B 162 " pdb=" CA PRO B 162 " ideal model delta harmonic sigma weight residual 180.00 153.24 26.76 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA THR B 68 " pdb=" C THR B 68 " pdb=" N TYR B 69 " pdb=" CA TYR B 69 " ideal model delta harmonic sigma weight residual -180.00 -157.49 -22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA THR A 32 " pdb=" C THR A 32 " pdb=" N VAL A 33 " pdb=" CA VAL A 33 " ideal model delta harmonic sigma weight residual 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 3784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 828 0.067 - 0.135: 132 0.135 - 0.202: 16 0.202 - 0.269: 1 0.269 - 0.336: 1 Chirality restraints: 978 Sorted by residual: chirality pdb=" C3' U r 2 " pdb=" C4' U r 2 " pdb=" O3' U r 2 " pdb=" C2' U r 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.14 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CB THR A 231 " pdb=" CA THR A 231 " pdb=" OG1 THR A 231 " pdb=" CG2 THR A 231 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA THR C 62 " pdb=" N THR C 62 " pdb=" C THR C 62 " pdb=" CB THR C 62 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 8.19e-01 ... (remaining 975 not shown) Planarity restraints: 1008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 13 " -0.080 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO A 14 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO A 14 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 14 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 198 " 0.060 5.00e-02 4.00e+02 9.11e-02 1.33e+01 pdb=" N PRO A 199 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 199 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 199 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 233 " 0.053 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO A 234 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " 0.044 5.00e-02 4.00e+02 ... (remaining 1005 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 837 2.76 - 3.29: 5650 3.29 - 3.83: 11067 3.83 - 4.36: 12501 4.36 - 4.90: 20514 Nonbonded interactions: 50569 Sorted by model distance: nonbonded pdb=" CB ALA A 258 " pdb=" SG CYS A 290 " model vdw 2.225 3.820 nonbonded pdb=" O ASP A 31 " pdb=" CG1 VAL A 58 " model vdw 2.235 3.460 nonbonded pdb=" N TYR A 59 " pdb=" CD PRO A 60 " model vdw 2.278 3.520 nonbonded pdb=" O PHE A 268 " pdb=" N6 A r 17 " model vdw 2.304 3.120 nonbonded pdb=" N GLN A 259 " pdb=" OE1 GLN A 259 " model vdw 2.316 3.120 ... (remaining 50564 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.410 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 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 : 0.009 0.585 6575 Z= 0.354 Angle : 0.932 10.118 9111 Z= 0.510 Chirality : 0.050 0.336 978 Planarity : 0.008 0.118 1008 Dihedral : 18.345 132.785 2581 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.91 % Favored : 93.93 % Rotamer: Outliers : 2.12 % Allowed : 27.43 % Favored : 70.44 % 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: -2.84 (0.30), residues: 626 helix: -1.56 (0.30), residues: 205 sheet: -1.40 (0.55), residues: 109 loop : -2.27 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 24 TYR 0.018 0.002 TYR A 219 PHE 0.034 0.002 PHE C 12 TRP 0.028 0.002 TRP A 211 HIS 0.007 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.24 ( 6570) covalent geometry : angle 0.93189 / 0.51 ( 9111) hydrogen bonds : bond 0.14650 / 9.49 ( 238) hydrogen bonds : angle 7.55533 / 5.20 ( 653) metal coordination : bond 0.28053 / 10.83 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7123 (t0) outliers start: 12 outliers final: 4 residues processed: 114 average time/residue: 0.1022 time to fit residues: 14.7098 Evaluate side-chains 59 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 266 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 ASN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.078795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.059678 restraints weight = 35017.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.061437 restraints weight = 18825.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.062569 restraints weight = 13294.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.063236 restraints weight = 10818.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.063644 restraints weight = 9589.181| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 6575 Z= 0.290 Angle : 0.783 9.119 9111 Z= 0.394 Chirality : 0.043 0.214 978 Planarity : 0.006 0.060 1008 Dihedral : 11.174 134.572 1275 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 6.02 % Allowed : 27.61 % Favored : 66.37 % 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: -2.02 (0.33), residues: 626 helix: -0.43 (0.34), residues: 218 sheet: -1.80 (0.48), residues: 125 loop : -1.77 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 168 TYR 0.024 0.002 TYR A 91 PHE 0.020 0.003 PHE C 18 TRP 0.021 0.002 TRP B 70 HIS 0.007 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.29 ( 6570) covalent geometry : angle 0.78256 / 0.39 ( 9111) hydrogen bonds : bond 0.06317 / 4.10 ( 238) hydrogen bonds : angle 5.74730 / 3.86 ( 653) metal coordination : bond 0.01013 / 0.53 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 56 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8414 (ptmm) REVERT: A 77 TRP cc_start: 0.8081 (t60) cc_final: 0.7784 (t-100) REVERT: A 86 TYR cc_start: 0.7869 (m-10) cc_final: 0.7526 (m-10) REVERT: A 197 MET cc_start: 0.8751 (ppp) cc_final: 0.8426 (ppp) REVERT: B 37 ASP cc_start: 0.7774 (t0) cc_final: 0.7470 (t0) REVERT: B 39 PHE cc_start: 0.8622 (m-80) cc_final: 0.8373 (m-80) REVERT: B 54 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8291 (tt0) outliers start: 34 outliers final: 16 residues processed: 84 average time/residue: 0.0776 time to fit residues: 8.6145 Evaluate side-chains 68 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 HIS ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.080160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.061397 restraints weight = 34299.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.063196 restraints weight = 18320.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.064341 restraints weight = 12883.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.065033 restraints weight = 10469.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.065443 restraints weight = 9233.678| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.248 6575 Z= 0.533 Angle : 0.627 9.078 9111 Z= 0.309 Chirality : 0.039 0.228 978 Planarity : 0.005 0.041 1008 Dihedral : 11.093 131.650 1271 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.96 % Allowed : 26.19 % Favored : 68.85 % 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: -1.67 (0.33), residues: 626 helix: -0.00 (0.35), residues: 214 sheet: -1.84 (0.45), residues: 139 loop : -1.49 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 375 TYR 0.011 0.001 TYR A 339 PHE 0.028 0.002 PHE C 12 TRP 0.011 0.001 TRP B 70 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 6570) covalent geometry : angle 0.62732 / 0.31 ( 9111) hydrogen bonds : bond 0.03895 / 2.58 ( 238) hydrogen bonds : angle 5.20414 / 3.47 ( 653) metal coordination : bond 0.55830 / 27.92 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 TYR cc_start: 0.7879 (m-10) cc_final: 0.7526 (m-10) REVERT: A 197 MET cc_start: 0.8729 (ppp) cc_final: 0.8352 (ppp) REVERT: A 337 MET cc_start: 0.7535 (mmm) cc_final: 0.7242 (mmm) REVERT: A 371 SER cc_start: 0.9299 (OUTLIER) cc_final: 0.9036 (p) REVERT: B 37 ASP cc_start: 0.7749 (t0) cc_final: 0.7514 (t0) REVERT: B 39 PHE cc_start: 0.8690 (m-80) cc_final: 0.8435 (m-80) REVERT: B 54 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8216 (tt0) REVERT: C 13 GLU cc_start: 0.9399 (mt-10) cc_final: 0.9049 (pp20) REVERT: C 67 GLN cc_start: 0.8742 (tp40) cc_final: 0.8405 (mm-40) outliers start: 28 outliers final: 19 residues processed: 81 average time/residue: 0.0822 time to fit residues: 8.9273 Evaluate side-chains 69 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 0.0470 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 overall best weight: 2.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS A 205 ASN A 301 ASN B 19 ASN C 45 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.075425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.056529 restraints weight = 35090.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.058198 restraints weight = 19187.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.059274 restraints weight = 13686.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.059932 restraints weight = 11244.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.060316 restraints weight = 9999.247| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 6575 Z= 0.304 Angle : 0.767 10.005 9111 Z= 0.385 Chirality : 0.043 0.219 978 Planarity : 0.005 0.050 1008 Dihedral : 12.197 131.076 1267 Min Nonbonded Distance : 1.599 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 6.73 % Allowed : 24.42 % Favored : 68.85 % 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: -1.72 (0.34), residues: 626 helix: -0.02 (0.35), residues: 209 sheet: -2.01 (0.47), residues: 133 loop : -1.46 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 375 TYR 0.016 0.002 TYR A 91 PHE 0.021 0.002 PHE A 164 TRP 0.013 0.002 TRP A 77 HIS 0.054 0.003 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.30 ( 6570) covalent geometry : angle 0.76668 / 0.38 ( 9111) hydrogen bonds : bond 0.06979 / 4.43 ( 238) hydrogen bonds : angle 5.60553 / 3.76 ( 653) metal coordination : bond 0.02263 / 1.17 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 48 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8316 (ppp) REVERT: B 39 PHE cc_start: 0.8676 (m-80) cc_final: 0.8367 (m-80) REVERT: C 39 GLU cc_start: 0.8798 (tp30) cc_final: 0.8464 (tt0) outliers start: 38 outliers final: 29 residues processed: 78 average time/residue: 0.0792 time to fit residues: 8.4043 Evaluate side-chains 75 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 45 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 55 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 61 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 0.0060 chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.077835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.059050 restraints weight = 35294.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.060870 restraints weight = 18956.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.062015 restraints weight = 13357.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.062684 restraints weight = 10857.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.063162 restraints weight = 9603.096| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6575 Z= 0.144 Angle : 0.627 10.603 9111 Z= 0.307 Chirality : 0.040 0.226 978 Planarity : 0.004 0.040 1008 Dihedral : 12.054 126.521 1267 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.49 % Allowed : 26.37 % Favored : 68.14 % 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: -1.45 (0.34), residues: 626 helix: 0.34 (0.36), residues: 210 sheet: -1.99 (0.44), residues: 142 loop : -1.31 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.011 0.001 TYR C 29 PHE 0.023 0.002 PHE C 12 TRP 0.011 0.001 TRP A 77 HIS 0.006 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 6570) covalent geometry : angle 0.62656 / 0.31 ( 9111) hydrogen bonds : bond 0.04255 / 2.79 ( 238) hydrogen bonds : angle 5.18404 / 3.43 ( 653) metal coordination : bond 0.03099 / 1.71 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 52 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: A 77 TRP cc_start: 0.8395 (t-100) cc_final: 0.8094 (t-100) REVERT: A 197 MET cc_start: 0.8780 (ppp) cc_final: 0.8344 (ppp) REVERT: A 337 MET cc_start: 0.7311 (mmm) cc_final: 0.7038 (mmm) REVERT: B 37 ASP cc_start: 0.7932 (t0) cc_final: 0.7628 (t0) REVERT: B 54 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8199 (tt0) REVERT: C 39 GLU cc_start: 0.8829 (tp30) cc_final: 0.8544 (tt0) outliers start: 31 outliers final: 21 residues processed: 77 average time/residue: 0.0773 time to fit residues: 8.0464 Evaluate side-chains 69 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 144 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.0470 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 ASN A 229 ASN ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.078191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.059572 restraints weight = 35024.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.061368 restraints weight = 18691.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.062501 restraints weight = 13228.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.063205 restraints weight = 10782.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.063612 restraints weight = 9521.280| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6575 Z= 0.141 Angle : 0.623 10.811 9111 Z= 0.302 Chirality : 0.039 0.219 978 Planarity : 0.004 0.032 1008 Dihedral : 11.869 124.417 1265 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.78 % Allowed : 26.90 % Favored : 68.32 % 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: -1.26 (0.34), residues: 626 helix: 0.55 (0.36), residues: 210 sheet: -1.85 (0.44), residues: 142 loop : -1.26 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 40 TYR 0.009 0.001 TYR B 30 PHE 0.020 0.002 PHE C 12 TRP 0.022 0.001 TRP A 77 HIS 0.005 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 6570) covalent geometry : angle 0.62261 / 0.30 ( 9111) hydrogen bonds : bond 0.04235 / 2.78 ( 238) hydrogen bonds : angle 5.09157 / 3.35 ( 653) metal coordination : bond 0.01460 / 0.82 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 52 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7901 (tt0) REVERT: A 197 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8357 (ppp) REVERT: B 37 ASP cc_start: 0.7847 (t0) cc_final: 0.7548 (t0) REVERT: B 54 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8169 (tt0) REVERT: C 39 GLU cc_start: 0.8819 (tp30) cc_final: 0.8601 (tt0) outliers start: 27 outliers final: 21 residues processed: 74 average time/residue: 0.0736 time to fit residues: 7.3666 Evaluate side-chains 74 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 51 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 144 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.076849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.058143 restraints weight = 34962.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.059906 restraints weight = 18958.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.061005 restraints weight = 13452.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.061666 restraints weight = 10993.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.062093 restraints weight = 9792.080| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6575 Z= 0.186 Angle : 0.639 8.032 9111 Z= 0.312 Chirality : 0.040 0.214 978 Planarity : 0.004 0.031 1008 Dihedral : 12.125 122.068 1265 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.13 % Allowed : 27.08 % Favored : 67.79 % 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: -1.06 (0.34), residues: 626 helix: 0.67 (0.36), residues: 210 sheet: -1.72 (0.46), residues: 133 loop : -1.16 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 40 TYR 0.013 0.001 TYR A 86 PHE 0.021 0.002 PHE C 12 TRP 0.013 0.001 TRP A 77 HIS 0.006 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 ( 6570) covalent geometry : angle 0.63914 / 0.31 ( 9111) hydrogen bonds : bond 0.04816 / 3.12 ( 238) hydrogen bonds : angle 5.16077 / 3.40 ( 653) metal coordination : bond 0.01389 / 0.79 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 54 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: A 122 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8192 (mtm-85) REVERT: A 197 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8284 (ppp) REVERT: B 37 ASP cc_start: 0.7941 (t0) cc_final: 0.7624 (t0) REVERT: B 54 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8249 (tt0) REVERT: C 35 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8789 (ptp-170) REVERT: C 122 MET cc_start: 0.8367 (mmm) cc_final: 0.8069 (tmm) outliers start: 29 outliers final: 23 residues processed: 77 average time/residue: 0.0783 time to fit residues: 8.0410 Evaluate side-chains 75 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 48 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 144 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.076932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.057578 restraints weight = 35825.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.059355 restraints weight = 19508.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.060450 restraints weight = 13986.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.061135 restraints weight = 11529.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.061488 restraints weight = 10269.571| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6575 Z= 0.211 Angle : 0.672 8.430 9111 Z= 0.330 Chirality : 0.040 0.209 978 Planarity : 0.004 0.032 1008 Dihedral : 12.468 119.068 1265 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.96 % Allowed : 27.43 % Favored : 67.61 % 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: -1.22 (0.34), residues: 626 helix: 0.54 (0.36), residues: 216 sheet: -1.97 (0.44), residues: 140 loop : -1.15 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 41 TYR 0.011 0.001 TYR A 91 PHE 0.020 0.002 PHE C 12 TRP 0.015 0.001 TRP A 77 HIS 0.008 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 ( 6570) covalent geometry : angle 0.67219 / 0.33 ( 9111) hydrogen bonds : bond 0.05278 / 3.42 ( 238) hydrogen bonds : angle 5.26455 / 3.48 ( 653) metal coordination : bond 0.01378 / 0.78 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 51 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: A 197 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8301 (ppp) REVERT: B 37 ASP cc_start: 0.7919 (t0) cc_final: 0.7621 (t0) REVERT: B 54 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8245 (tt0) REVERT: C 39 GLU cc_start: 0.8955 (tp30) cc_final: 0.8582 (tt0) outliers start: 28 outliers final: 23 residues processed: 73 average time/residue: 0.0766 time to fit residues: 7.5677 Evaluate side-chains 76 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 51 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 144 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 0.0170 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.7220 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.077566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.059051 restraints weight = 34756.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.060915 restraints weight = 18619.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.062021 restraints weight = 13032.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.062745 restraints weight = 10599.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.063139 restraints weight = 9374.221| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6575 Z= 0.135 Angle : 0.640 9.403 9111 Z= 0.309 Chirality : 0.040 0.204 978 Planarity : 0.004 0.042 1008 Dihedral : 12.248 116.268 1265 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.07 % Allowed : 27.96 % Favored : 67.96 % 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: -1.02 (0.35), residues: 626 helix: 0.60 (0.35), residues: 219 sheet: -1.64 (0.47), residues: 133 loop : -1.13 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 40 TYR 0.013 0.001 TYR A 86 PHE 0.018 0.002 PHE C 12 TRP 0.014 0.001 TRP A 77 HIS 0.004 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 6570) covalent geometry : angle 0.64009 / 0.31 ( 9111) hydrogen bonds : bond 0.04186 / 2.75 ( 238) hydrogen bonds : angle 5.03462 / 3.30 ( 653) metal coordination : bond 0.00868 / 0.49 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: A 197 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8320 (ppp) REVERT: B 37 ASP cc_start: 0.7917 (t0) cc_final: 0.7618 (t0) REVERT: B 54 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8171 (tt0) REVERT: C 39 GLU cc_start: 0.8959 (tp30) cc_final: 0.8565 (tt0) REVERT: C 122 MET cc_start: 0.8356 (mmm) cc_final: 0.7961 (tmm) outliers start: 23 outliers final: 19 residues processed: 71 average time/residue: 0.0834 time to fit residues: 7.8450 Evaluate side-chains 69 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 144 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.078579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.059540 restraints weight = 34943.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.061348 restraints weight = 18827.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.062467 restraints weight = 13400.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.063120 restraints weight = 10989.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.063556 restraints weight = 9793.280| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6575 Z= 0.139 Angle : 0.653 9.491 9111 Z= 0.317 Chirality : 0.040 0.196 978 Planarity : 0.004 0.044 1008 Dihedral : 12.132 116.166 1265 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.72 % Allowed : 28.85 % Favored : 67.43 % 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: -0.94 (0.35), residues: 626 helix: 0.68 (0.36), residues: 217 sheet: -1.49 (0.47), residues: 133 loop : -1.14 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 9 TYR 0.010 0.001 TYR B 30 PHE 0.013 0.002 PHE A 164 TRP 0.015 0.001 TRP A 77 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 6570) covalent geometry : angle 0.65255 / 0.32 ( 9111) hydrogen bonds : bond 0.04460 / 2.92 ( 238) hydrogen bonds : angle 5.03494 / 3.29 ( 653) metal coordination : bond 0.00879 / 0.50 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: A 197 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8311 (ppp) REVERT: B 54 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8168 (tt0) REVERT: C 39 GLU cc_start: 0.8950 (tp30) cc_final: 0.8544 (tt0) REVERT: C 122 MET cc_start: 0.8367 (mmm) cc_final: 0.7981 (tmm) outliers start: 21 outliers final: 18 residues processed: 65 average time/residue: 0.0633 time to fit residues: 5.7274 Evaluate side-chains 67 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.077273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.058740 restraints weight = 34291.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.060539 restraints weight = 18509.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.061657 restraints weight = 13063.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.062322 restraints weight = 10632.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.062742 restraints weight = 9412.920| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6575 Z= 0.153 Angle : 0.650 9.287 9111 Z= 0.317 Chirality : 0.040 0.192 978 Planarity : 0.004 0.040 1008 Dihedral : 12.122 115.914 1265 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.89 % Allowed : 28.50 % Favored : 67.61 % 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: -0.89 (0.35), residues: 626 helix: 0.73 (0.36), residues: 217 sheet: -1.46 (0.47), residues: 133 loop : -1.12 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 9 TYR 0.016 0.001 TYR A 86 PHE 0.013 0.002 PHE A 164 TRP 0.019 0.001 TRP A 77 HIS 0.004 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 6570) covalent geometry : angle 0.64978 / 0.32 ( 9111) hydrogen bonds : bond 0.04565 / 2.98 ( 238) hydrogen bonds : angle 5.03653 / 3.29 ( 653) metal coordination : bond 0.00926 / 0.52 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1390.49 seconds wall clock time: 24 minutes 34.62 seconds (1474.62 seconds total)