Starting phenix.real_space_refine on Sat Aug 23 03:50:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e40_27875/08_2025/8e40_27875.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e40_27875/08_2025/8e40_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 { model { file = "/net/cci-nas-00/data/ceres_data/8e40_27875/08_2025/8e40_27875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e40_27875/08_2025/8e40_27875.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e40_27875/08_2025/8e40_27875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e40_27875/08_2025/8e40_27875.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 1.64, 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: 0.51 Conformation dependent library (CDL) restraints added in 326.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.69 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: 1.08 Time building geometry restraints manager: 0.65 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: 3447 26.56 - 53.11: 357 53.11 - 79.67: 65 79.67 - 106.23: 4 106.23 - 132.79: 2 Dihedral angle restraints: 3875 sinusoidal: 2013 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 3872 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: 4.160 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.550 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 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 : 19.336 132.785 2669 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 aren 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 covalent geometry : bond 0.00520 ( 6570) covalent geometry : angle 0.93189 ( 9111) hydrogen bonds : bond 0.14650 ( 238) hydrogen bonds : angle 7.55533 ( 653) metal coordination : bond 0.28053 ( 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 : 0.204 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: 0.1028 time to fit residues: 14.6540 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 : 0.144 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4113 r_free = 0.4113 target = 0.079022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.059871 restraints weight = 34992.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.061645 restraints weight = 18845.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.062772 restraints weight = 13304.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.063455 restraints weight = 10822.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.063882 restraints weight = 9571.596| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 6575 Z= 0.279 Angle : 0.766 9.034 9111 Z= 0.386 Chirality : 0.042 0.213 978 Planarity : 0.006 0.061 1008 Dihedral : 14.627 134.925 1363 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.49 % Allowed : 27.43 % Favored : 67.08 % 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: -2.04 (0.32), residues: 626 helix: -0.47 (0.34), residues: 218 sheet: -1.76 (0.48), residues: 124 loop : -1.80 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 15 TYR 0.023 0.002 TYR A 91 PHE 0.019 0.003 PHE A 241 TRP 0.020 0.002 TRP B 70 HIS 0.007 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00610 ( 6570) covalent geometry : angle 0.76573 ( 9111) hydrogen bonds : bond 0.06206 ( 238) hydrogen bonds : angle 5.75900 ( 653) metal coordination : bond 0.01202 ( 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 87 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 56 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 TRP cc_start: 0.8067 (t60) cc_final: 0.7797 (t-100) REVERT: A 86 TYR cc_start: 0.7840 (m-10) cc_final: 0.7503 (m-10) REVERT: A 197 MET cc_start: 0.8717 (ppp) cc_final: 0.8419 (ppp) REVERT: A 264 ASP cc_start: 0.9085 (OUTLIER) cc_final: 0.8878 (t0) REVERT: B 37 ASP cc_start: 0.7719 (t0) cc_final: 0.7414 (t0) REVERT: B 39 PHE cc_start: 0.8621 (m-80) cc_final: 0.8380 (m-80) REVERT: B 54 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8280 (tt0) REVERT: C 13 GLU cc_start: 0.9365 (mt-10) cc_final: 0.9049 (pp20) outliers start: 31 outliers final: 15 residues processed: 81 average time/residue: 0.0777 time to fit residues: 8.3241 Evaluate side-chains 67 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 122 ARG Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 264 ASP 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: 0.7980 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 30 optimal weight: 2.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4154 r_free = 0.4154 target = 0.080745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.061958 restraints weight = 34329.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.063828 restraints weight = 18155.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.064986 restraints weight = 12695.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.065715 restraints weight = 10289.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.066140 restraints weight = 9037.126| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.246 6575 Z= 0.529 Angle : 0.619 9.097 9111 Z= 0.304 Chirality : 0.039 0.229 978 Planarity : 0.004 0.041 1008 Dihedral : 14.467 131.774 1357 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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 aren not related in a simple way. whole: -1.66 (0.33), residues: 626 helix: 0.04 (0.35), residues: 219 sheet: -1.80 (0.45), residues: 139 loop : -1.57 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 375 TYR 0.011 0.001 TYR A 339 PHE 0.018 0.002 PHE A 164 TRP 0.011 0.001 TRP B 70 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6570) covalent geometry : angle 0.61880 ( 9111) hydrogen bonds : bond 0.03801 ( 238) hydrogen bonds : angle 5.15984 ( 653) metal coordination : bond 0.55744 ( 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 87 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 59 time to evaluate : 0.232 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: 0.7870 (m-10) cc_final: 0.7516 (m-10) REVERT: A 197 MET cc_start: 0.8690 (ppp) cc_final: 0.8279 (ppp) REVERT: A 337 MET cc_start: 0.7526 (mmm) cc_final: 0.7293 (mmm) REVERT: A 371 SER cc_start: 0.9300 (OUTLIER) cc_final: 0.9038 (p) REVERT: B 37 ASP cc_start: 0.7734 (t0) cc_final: 0.7506 (t0) REVERT: B 39 PHE cc_start: 0.8671 (m-80) cc_final: 0.8429 (m-80) REVERT: B 54 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8218 (tt0) REVERT: C 13 GLU cc_start: 0.9387 (mt-10) cc_final: 0.9031 (pp20) REVERT: C 67 GLN cc_start: 0.8745 (tp40) cc_final: 0.8410 (mm-40) outliers start: 28 outliers final: 18 residues processed: 82 average time/residue: 0.0854 time to fit residues: 9.1465 Evaluate side-chains 70 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 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 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 10 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 ASN C 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.077560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.058562 restraints weight = 34811.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.060324 restraints weight = 18883.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.061420 restraints weight = 13431.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.062087 restraints weight = 11003.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.062518 restraints weight = 9775.198| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 6575 Z= 0.258 Angle : 0.698 9.865 9111 Z= 0.350 Chirality : 0.042 0.234 978 Planarity : 0.005 0.059 1008 Dihedral : 14.902 131.544 1353 Min Nonbonded Distance : 1.275 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 6.55 % Allowed : 24.42 % Favored : 69.03 % 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: -1.74 (0.33), residues: 626 helix: 0.13 (0.35), residues: 220 sheet: -2.00 (0.45), residues: 135 loop : -1.69 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 375 TYR 0.014 0.002 TYR A 91 PHE 0.023 0.002 PHE A 241 TRP 0.011 0.002 TRP A 77 HIS 0.058 0.003 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 6570) covalent geometry : angle 0.69822 ( 9111) hydrogen bonds : bond 0.05456 ( 238) hydrogen bonds : angle 5.28579 ( 653) metal coordination : bond 0.03613 ( 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 88 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 51 time to evaluate : 0.228 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: 0.7943 (m-10) cc_final: 0.7694 (m-10) REVERT: A 122 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8139 (mtm-85) REVERT: A 197 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8315 (ppp) REVERT: B 37 ASP cc_start: 0.7813 (t0) cc_final: 0.7555 (t0) REVERT: B 54 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8211 (tt0) REVERT: B 96 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7937 (m) outliers start: 37 outliers final: 26 residues processed: 81 average time/residue: 0.0800 time to fit residues: 8.7654 Evaluate side-chains 77 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 48 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 THR 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 231 THR Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 276 TYR 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 8 MET Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 96 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 34 optimal weight: 0.0170 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.079617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.060910 restraints weight = 34673.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.062774 restraints weight = 18382.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.063914 restraints weight = 12918.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.064585 restraints weight = 10504.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.065034 restraints weight = 9295.373| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 6575 Z= 0.133 Angle : 0.613 10.943 9111 Z= 0.301 Chirality : 0.040 0.226 978 Planarity : 0.004 0.051 1008 Dihedral : 14.678 128.068 1353 Min Nonbonded Distance : 1.285 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.49 % Allowed : 24.96 % Favored : 69.56 % 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: -1.37 (0.34), residues: 626 helix: 0.32 (0.35), residues: 215 sheet: -1.77 (0.45), residues: 141 loop : -1.33 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.008 0.001 TYR A 339 PHE 0.017 0.002 PHE A 241 TRP 0.012 0.001 TRP A 77 HIS 0.046 0.002 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6570) covalent geometry : angle 0.61260 ( 9111) hydrogen bonds : bond 0.03709 ( 238) hydrogen bonds : angle 4.96199 ( 653) metal coordination : bond 0.05535 ( 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 89 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 58 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7885 (tt0) REVERT: A 197 MET cc_start: 0.8723 (ppp) cc_final: 0.8321 (ppp) REVERT: A 337 MET cc_start: 0.7476 (mmm) cc_final: 0.7185 (mmm) REVERT: B 37 ASP cc_start: 0.7832 (t0) cc_final: 0.7578 (t0) REVERT: B 54 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8207 (tt0) REVERT: C 67 GLN cc_start: 0.8850 (tp40) cc_final: 0.8548 (mm-40) outliers start: 31 outliers final: 19 residues processed: 84 average time/residue: 0.0795 time to fit residues: 8.8149 Evaluate side-chains 70 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 231 THR Chi-restraints excluded: chain A residue 257 HIS 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.0770 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 205 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 = 0.4123 r_free = 0.4123 target = 0.078897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.060197 restraints weight = 34725.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.061993 restraints weight = 18763.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.063120 restraints weight = 13265.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.063806 restraints weight = 10842.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.064249 restraints weight = 9589.756| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 6575 Z= 0.159 Angle : 0.630 10.655 9111 Z= 0.309 Chirality : 0.040 0.219 978 Planarity : 0.004 0.048 1008 Dihedral : 14.650 127.395 1353 Min Nonbonded Distance : 1.314 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.49 % Allowed : 26.19 % 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 aren not related in a simple way. whole: -1.25 (0.34), residues: 626 helix: 0.54 (0.35), residues: 216 sheet: -1.79 (0.44), residues: 143 loop : -1.32 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 40 TYR 0.009 0.001 TYR A 182 PHE 0.018 0.002 PHE A 164 TRP 0.009 0.001 TRP A 77 HIS 0.044 0.002 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6570) covalent geometry : angle 0.62970 ( 9111) hydrogen bonds : bond 0.04271 ( 238) hydrogen bonds : angle 4.99907 ( 653) metal coordination : bond 0.04459 ( 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 82 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 51 time to evaluate : 0.264 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: 0.8349 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: A 197 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8410 (ppp) REVERT: A 337 MET cc_start: 0.7378 (mmm) cc_final: 0.7138 (mmm) REVERT: B 54 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8188 (tt0) outliers start: 31 outliers final: 25 residues processed: 75 average time/residue: 0.0746 time to fit residues: 7.4907 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 : 0.199 ------------------------------------------------------------------------------- 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 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 138 LEU 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 197 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 324 LEU 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 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: 0.8980 chunk 64 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 303 HIS ** 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 = 0.4078 r_free = 0.4078 target = 0.076713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.058017 restraints weight = 35044.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.059755 restraints weight = 18822.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.060872 restraints weight = 13406.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.061562 restraints weight = 10952.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.061953 restraints weight = 9691.147| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 6575 Z= 0.215 Angle : 0.677 12.436 9111 Z= 0.334 Chirality : 0.040 0.217 978 Planarity : 0.004 0.045 1008 Dihedral : 15.150 125.284 1353 Min Nonbonded Distance : 1.344 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.66 % Allowed : 26.37 % 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 aren not related in a simple way. whole: -1.21 (0.34), residues: 626 helix: 0.51 (0.35), residues: 217 sheet: -1.92 (0.44), residues: 140 loop : -1.14 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 33 TYR 0.016 0.002 TYR A 86 PHE 0.019 0.002 PHE C 12 TRP 0.010 0.001 TRP A 77 HIS 0.040 0.002 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 6570) covalent geometry : angle 0.67726 ( 9111) hydrogen bonds : bond 0.05080 ( 238) hydrogen bonds : angle 5.27194 ( 653) metal coordination : bond 0.04013 ( 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 80 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 48 time to evaluate : 0.146 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: 0.8395 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: A 197 MET cc_start: 0.8781 (ppp) cc_final: 0.8270 (ppp) REVERT: A 337 MET cc_start: 0.7244 (mmm) cc_final: 0.7025 (mmm) REVERT: B 37 ASP cc_start: 0.7880 (t0) cc_final: 0.7587 (t0) REVERT: B 54 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8233 (tt0) outliers start: 32 outliers final: 26 residues processed: 74 average time/residue: 0.0675 time to fit residues: 6.7806 Evaluate side-chains 72 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 45 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 88 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 LEU 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 231 THR Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 276 TYR 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 8 MET 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 106 VAL 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: 7.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.0010 chunk 61 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.079374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.060900 restraints weight = 34882.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.062774 restraints weight = 18353.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.063953 restraints weight = 12847.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.064618 restraints weight = 10412.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.065084 restraints weight = 9207.609| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 6575 Z= 0.123 Angle : 0.620 9.036 9111 Z= 0.301 Chirality : 0.039 0.218 978 Planarity : 0.004 0.041 1008 Dihedral : 14.835 122.100 1353 Min Nonbonded Distance : 1.306 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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 aren not related in a simple way. whole: -1.03 (0.35), residues: 626 helix: 0.61 (0.36), residues: 222 sheet: -1.47 (0.47), residues: 133 loop : -1.28 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 122 TYR 0.010 0.001 TYR A 339 PHE 0.016 0.002 PHE C 12 TRP 0.015 0.001 TRP A 94 HIS 0.038 0.002 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6570) covalent geometry : angle 0.62045 ( 9111) hydrogen bonds : bond 0.03695 ( 238) hydrogen bonds : angle 4.93245 ( 653) metal coordination : bond 0.04873 ( 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 80 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: A 197 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8355 (ppp) REVERT: A 337 MET cc_start: 0.7133 (mmm) cc_final: 0.6931 (mmm) REVERT: B 37 ASP cc_start: 0.7740 (t0) cc_final: 0.7478 (t0) REVERT: B 54 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8209 (tt0) REVERT: C 67 GLN cc_start: 0.8915 (tp40) cc_final: 0.8594 (mm-40) outliers start: 23 outliers final: 20 residues processed: 73 average time/residue: 0.0769 time to fit residues: 7.4546 Evaluate side-chains 73 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL 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 138 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.078671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.060007 restraints weight = 35200.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.061838 restraints weight = 18486.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.062990 restraints weight = 12968.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.063684 restraints weight = 10553.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.064098 restraints weight = 9323.237| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6575 Z= 0.141 Angle : 0.643 11.916 9111 Z= 0.312 Chirality : 0.039 0.212 978 Planarity : 0.004 0.034 1008 Dihedral : 14.812 121.485 1353 Min Nonbonded Distance : 1.365 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.42 % Allowed : 28.14 % 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 aren not related in a simple way. whole: -0.94 (0.35), residues: 626 helix: 0.74 (0.36), residues: 219 sheet: -1.46 (0.47), residues: 133 loop : -1.23 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 83 TYR 0.013 0.001 TYR A 86 PHE 0.012 0.002 PHE A 164 TRP 0.014 0.001 TRP A 77 HIS 0.032 0.002 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 6570) covalent geometry : angle 0.64305 ( 9111) hydrogen bonds : bond 0.04236 ( 238) hydrogen bonds : angle 4.91223 ( 653) metal coordination : bond 0.03127 ( 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: 25 poor density : 51 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.5108 (OUTLIER) cc_final: 0.4407 (pm20) REVERT: A 55 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: A 197 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8328 (ppp) REVERT: A 337 MET cc_start: 0.7206 (mmm) cc_final: 0.6853 (mmm) REVERT: B 37 ASP cc_start: 0.7857 (t0) cc_final: 0.7596 (t0) REVERT: B 54 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8214 (tt0) outliers start: 25 outliers final: 22 residues processed: 69 average time/residue: 0.0606 time to fit residues: 5.8807 Evaluate side-chains 75 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 50 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU 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 138 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 257 HIS 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 106 VAL 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: 2.9990 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 60 optimal weight: 0.0770 chunk 36 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.079335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.060816 restraints weight = 34760.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.062698 restraints weight = 18379.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.063872 restraints weight = 12864.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.064548 restraints weight = 10448.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.065001 restraints weight = 9222.735| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6575 Z= 0.128 Angle : 0.633 11.803 9111 Z= 0.307 Chirality : 0.039 0.210 978 Planarity : 0.004 0.032 1008 Dihedral : 14.612 119.217 1353 Min Nonbonded Distance : 1.381 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.07 % Allowed : 28.14 % 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 aren not related in a simple way. whole: -0.83 (0.35), residues: 626 helix: 0.82 (0.36), residues: 219 sheet: -1.36 (0.48), residues: 131 loop : -1.19 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 23 TYR 0.009 0.001 TYR C 29 PHE 0.013 0.002 PHE B 39 TRP 0.014 0.001 TRP A 77 HIS 0.031 0.002 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 6570) covalent geometry : angle 0.63344 ( 9111) hydrogen bonds : bond 0.03913 ( 238) hydrogen bonds : angle 4.84196 ( 653) metal coordination : bond 0.02890 ( 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 77 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8321 (ppp) REVERT: A 337 MET cc_start: 0.7240 (mmm) cc_final: 0.6936 (mmm) REVERT: B 37 ASP cc_start: 0.7802 (t0) cc_final: 0.7542 (t0) REVERT: B 54 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8221 (tt0) REVERT: C 67 GLN cc_start: 0.8967 (tp40) cc_final: 0.8620 (mm-40) outliers start: 23 outliers final: 20 residues processed: 70 average time/residue: 0.0756 time to fit residues: 7.1165 Evaluate side-chains 71 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 138 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 287 CYS 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 106 VAL 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: 3.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.077208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.058512 restraints weight = 35125.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.060351 restraints weight = 18762.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.061454 restraints weight = 13237.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.062145 restraints weight = 10819.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.062548 restraints weight = 9616.422| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6575 Z= 0.200 Angle : 0.681 9.085 9111 Z= 0.334 Chirality : 0.040 0.206 978 Planarity : 0.004 0.033 1008 Dihedral : 14.921 118.948 1353 Min Nonbonded Distance : 1.409 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.60 % Allowed : 27.79 % 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 aren not related in a simple way. whole: -0.79 (0.35), residues: 626 helix: 1.02 (0.37), residues: 213 sheet: -1.55 (0.46), residues: 131 loop : -1.16 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 83 TYR 0.014 0.001 TYR A 86 PHE 0.014 0.002 PHE A 164 TRP 0.018 0.001 TRP A 77 HIS 0.031 0.002 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 6570) covalent geometry : angle 0.68066 ( 9111) hydrogen bonds : bond 0.05116 ( 238) hydrogen bonds : angle 5.05641 ( 653) metal coordination : bond 0.02228 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1431.14 seconds wall clock time: 25 minutes 15.74 seconds (1515.74 seconds total)