Starting phenix.real_space_refine on Thu Jul 2 01:35:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wxr_66355/07_2026/9wxr_66355.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wxr_66355/07_2026/9wxr_66355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wxr_66355/07_2026/9wxr_66355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wxr_66355/07_2026/9wxr_66355.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wxr_66355/07_2026/9wxr_66355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wxr_66355/07_2026/9wxr_66355.map" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 3370 2.51 5 N 824 2.21 5 O 956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5166 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2563 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 8, 'TRANS': 336} Chain breaks: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Restraints were copied for chains: B Time building chain proxies: 1.71, per 1000 atoms: 0.33 Number of scatterers: 5166 At special positions: 0 Unit cell: (64.38, 93.98, 115.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 956 8.00 N 824 7.00 C 3370 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 243.2 milliseconds 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1244 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 87.2% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 2 through 28 removed outlier: 3.853A pdb=" N VAL A 6 " --> pdb=" O ASP A 2 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL A 7 " --> pdb=" O ALA A 3 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 22 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 42 through 58 Processing helix chain 'A' and resid 71 through 93 removed outlier: 3.979A pdb=" N TRP A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.533A pdb=" N ILE A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 119 removed outlier: 4.009A pdb=" N ILE A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 145 removed outlier: 3.855A pdb=" N TRP A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N HIS A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 137 " --> pdb=" O MET A 133 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 150 removed outlier: 3.766A pdb=" N VAL A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 181 removed outlier: 4.338A pdb=" N ILE A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Proline residue: A 175 - end of helix Processing helix chain 'A' and resid 189 through 215 Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 216 through 219 Processing helix chain 'A' and resid 248 through 255 Processing helix chain 'A' and resid 255 through 279 removed outlier: 4.150A pdb=" N LYS A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 319 removed outlier: 3.922A pdb=" N ALA A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLU A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR A 303 " --> pdb=" O ASN A 299 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 370 Processing helix chain 'B' and resid 2 through 28 removed outlier: 3.852A pdb=" N VAL B 6 " --> pdb=" O ASP B 2 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL B 7 " --> pdb=" O ALA B 3 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 42 through 58 Processing helix chain 'B' and resid 71 through 93 removed outlier: 3.980A pdb=" N TRP B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 78 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Proline residue: B 82 - end of helix removed outlier: 3.533A pdb=" N ILE B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 119 removed outlier: 4.009A pdb=" N ILE B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 145 removed outlier: 3.855A pdb=" N TRP B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N HIS B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 137 " --> pdb=" O MET B 133 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.765A pdb=" N VAL B 150 " --> pdb=" O PRO B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 181 removed outlier: 4.338A pdb=" N ILE B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Proline residue: B 175 - end of helix Processing helix chain 'B' and resid 189 through 215 Proline residue: B 207 - end of helix Processing helix chain 'B' and resid 216 through 219 Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 255 through 279 removed outlier: 4.150A pdb=" N LYS B 259 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 260 " --> pdb=" O TYR B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 319 removed outlier: 3.922A pdb=" N ALA B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLU B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR B 303 " --> pdb=" O ASN B 299 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 370 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 64 Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 64 428 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.72 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1304 1.33 - 1.45: 987 1.45 - 1.57: 2937 1.57 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 5260 Sorted by residual: bond pdb=" CB MET A 109 " pdb=" CG MET A 109 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.54e-01 bond pdb=" CB MET B 109 " pdb=" CG MET B 109 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.49e-01 bond pdb=" CD GLN A 364 " pdb=" OE1 GLN A 364 " ideal model delta sigma weight residual 1.231 1.215 0.016 1.90e-02 2.77e+03 6.98e-01 bond pdb=" CD GLN B 364 " pdb=" OE1 GLN B 364 " ideal model delta sigma weight residual 1.231 1.216 0.015 1.90e-02 2.77e+03 6.35e-01 bond pdb=" SD MET B 109 " pdb=" CE MET B 109 " ideal model delta sigma weight residual 1.791 1.772 0.019 2.50e-02 1.60e+03 6.03e-01 ... (remaining 5255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 7033 1.89 - 3.78: 107 3.78 - 5.67: 30 5.67 - 7.56: 4 7.56 - 9.45: 4 Bond angle restraints: 7178 Sorted by residual: angle pdb=" N GLN A 364 " pdb=" CA GLN A 364 " pdb=" CB GLN A 364 " ideal model delta sigma weight residual 110.28 115.25 -4.97 1.55e+00 4.16e-01 1.03e+01 angle pdb=" N GLN B 364 " pdb=" CA GLN B 364 " pdb=" CB GLN B 364 " ideal model delta sigma weight residual 110.28 115.23 -4.95 1.55e+00 4.16e-01 1.02e+01 angle pdb=" CB MET A 109 " pdb=" CG MET A 109 " pdb=" SD MET A 109 " ideal model delta sigma weight residual 112.70 103.25 9.45 3.00e+00 1.11e-01 9.93e+00 angle pdb=" CB MET B 109 " pdb=" CG MET B 109 " pdb=" SD MET B 109 " ideal model delta sigma weight residual 112.70 103.29 9.41 3.00e+00 1.11e-01 9.84e+00 angle pdb=" CA MET B 355 " pdb=" CB MET B 355 " pdb=" CG MET B 355 " ideal model delta sigma weight residual 114.10 119.05 -4.95 2.00e+00 2.50e-01 6.12e+00 ... (remaining 7173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 2778 17.50 - 35.00: 216 35.00 - 52.50: 26 52.50 - 70.00: 0 70.00 - 87.50: 8 Dihedral angle restraints: 3028 sinusoidal: 1068 harmonic: 1960 Sorted by residual: dihedral pdb=" CA ALA B 132 " pdb=" C ALA B 132 " pdb=" N MET B 133 " pdb=" CA MET B 133 " ideal model delta harmonic sigma weight residual -180.00 -159.77 -20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ALA A 132 " pdb=" C ALA A 132 " pdb=" N MET A 133 " pdb=" CA MET A 133 " ideal model delta harmonic sigma weight residual -180.00 -159.78 -20.22 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ALA B 300 " pdb=" C ALA B 300 " pdb=" N ALA B 301 " pdb=" CA ALA B 301 " ideal model delta harmonic sigma weight residual -180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 3025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 567 0.033 - 0.067: 219 0.067 - 0.100: 64 0.100 - 0.133: 22 0.133 - 0.167: 6 Chirality restraints: 878 Sorted by residual: chirality pdb=" CG LEU B 352 " pdb=" CB LEU B 352 " pdb=" CD1 LEU B 352 " pdb=" CD2 LEU B 352 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CG LEU A 352 " pdb=" CB LEU A 352 " pdb=" CD1 LEU A 352 " pdb=" CD2 LEU A 352 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CG LEU B 292 " pdb=" CB LEU B 292 " pdb=" CD1 LEU B 292 " pdb=" CD2 LEU B 292 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 875 not shown) Planarity restraints: 894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 355 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C MET B 355 " -0.025 2.00e-02 2.50e+03 pdb=" O MET B 355 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU B 356 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 355 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C MET A 355 " 0.025 2.00e-02 2.50e+03 pdb=" O MET A 355 " -0.009 2.00e-02 2.50e+03 pdb=" N GLU A 356 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 208 " 0.014 2.00e-02 2.50e+03 9.34e-03 1.74e+00 pdb=" CG TYR B 208 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 208 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 208 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 208 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 208 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 208 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 208 " -0.001 2.00e-02 2.50e+03 ... (remaining 891 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 2090 2.89 - 3.39: 6168 3.39 - 3.90: 8536 3.90 - 4.40: 9733 4.40 - 4.90: 15006 Nonbonded interactions: 41533 Sorted by model distance: nonbonded pdb=" O ALA A 360 " pdb=" OE1 GLN A 364 " model vdw 2.391 3.040 nonbonded pdb=" O ALA B 360 " pdb=" OE1 GLN B 364 " model vdw 2.392 3.040 nonbonded pdb=" O ASP A 321 " pdb=" OD1 ASP A 321 " model vdw 2.553 3.040 nonbonded pdb=" O ASP B 321 " pdb=" OD1 ASP B 321 " model vdw 2.554 3.040 nonbonded pdb=" O MET B 103 " pdb=" OD1 ASP B 106 " model vdw 2.580 3.040 ... (remaining 41528 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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: 7.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.110 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 : 0.003 0.028 5262 Z= 0.152 Angle : 0.664 9.452 7178 Z= 0.346 Chirality : 0.042 0.167 878 Planarity : 0.004 0.032 894 Dihedral : 12.809 87.499 1784 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.31 (0.31), residues: 682 helix: 1.08 (0.22), residues: 536 sheet: None (None), residues: 0 loop : 0.45 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 351 TYR 0.021 0.002 TYR B 208 PHE 0.008 0.001 PHE A 212 TRP 0.012 0.001 TRP A 171 HIS 0.002 0.001 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 ( 5260) covalent geometry : angle 0.66411 / 0.35 ( 7178) hydrogen bonds : bond 0.11735 / 8.33 ( 428) hydrogen bonds : angle 6.06796 / 4.44 ( 1266) Misc. bond : bond 0.00051 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.9570 (mmm) cc_final: 0.9363 (mmm) REVERT: A 293 LEU cc_start: 0.9780 (mm) cc_final: 0.9441 (tt) REVERT: A 328 SER cc_start: 0.7899 (t) cc_final: 0.7570 (p) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0505 time to fit residues: 5.0689 Evaluate side-chains 64 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.066677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.049823 restraints weight = 18692.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.050979 restraints weight = 14041.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.051820 restraints weight = 11463.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.052553 restraints weight = 9965.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.053122 restraints weight = 8898.383| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5262 Z= 0.134 Angle : 0.596 8.084 7178 Z= 0.305 Chirality : 0.041 0.128 878 Planarity : 0.004 0.030 894 Dihedral : 6.565 86.061 764 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.38 % Allowed : 2.28 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.31), residues: 682 helix: 1.12 (0.21), residues: 564 sheet: None (None), residues: 0 loop : 0.78 (0.50), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 351 TYR 0.023 0.002 TYR B 208 PHE 0.007 0.001 PHE B 212 TRP 0.008 0.001 TRP B 171 HIS 0.005 0.002 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 5260) covalent geometry : angle 0.59647 / 0.30 ( 7178) hydrogen bonds : bond 0.04213 / 2.87 ( 428) hydrogen bonds : angle 4.49935 / 3.28 ( 1266) Misc. bond : bond 0.00016 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.9151 (mmt) cc_final: 0.8225 (mmt) REVERT: A 135 HIS cc_start: 0.9445 (t-90) cc_final: 0.9052 (m90) REVERT: A 199 PHE cc_start: 0.9350 (t80) cc_final: 0.9133 (t80) outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.0604 time to fit residues: 4.9899 Evaluate side-chains 55 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 8 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.0020 chunk 15 optimal weight: 6.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.068510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.052168 restraints weight = 19162.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.053456 restraints weight = 13869.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.054488 restraints weight = 11120.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.055244 restraints weight = 9425.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.055688 restraints weight = 8329.438| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5262 Z= 0.137 Angle : 0.667 6.786 7178 Z= 0.330 Chirality : 0.040 0.133 878 Planarity : 0.004 0.028 894 Dihedral : 6.251 59.135 764 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.76 % Allowed : 5.32 % Favored : 93.92 % 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: 1.31 (0.32), residues: 682 helix: 0.97 (0.22), residues: 558 sheet: None (None), residues: 0 loop : 0.91 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 351 TYR 0.019 0.002 TYR B 208 PHE 0.012 0.001 PHE B 212 TRP 0.007 0.001 TRP B 77 HIS 0.007 0.004 HIS B 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 5260) covalent geometry : angle 0.66706 / 0.33 ( 7178) hydrogen bonds : bond 0.04010 / 2.72 ( 428) hydrogen bonds : angle 4.34181 / 3.17 ( 1266) Misc. bond : bond 0.00206 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LEU cc_start: 0.9289 (mm) cc_final: 0.9089 (mm) REVERT: A 171 TRP cc_start: 0.8574 (t-100) cc_final: 0.8209 (t-100) REVERT: A 199 PHE cc_start: 0.9230 (t80) cc_final: 0.8850 (t80) outliers start: 2 outliers final: 1 residues processed: 63 average time/residue: 0.0537 time to fit residues: 4.1536 Evaluate side-chains 52 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 65 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 4 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 6 optimal weight: 0.0670 chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 23 optimal weight: 0.0040 overall best weight: 1.2312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.069276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.053557 restraints weight = 22069.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.054876 restraints weight = 16447.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.055808 restraints weight = 13187.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.056487 restraints weight = 11162.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.057027 restraints weight = 9835.193| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5262 Z= 0.162 Angle : 0.753 9.137 7178 Z= 0.371 Chirality : 0.042 0.126 878 Planarity : 0.004 0.031 894 Dihedral : 7.167 86.710 764 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 1.00 (0.32), residues: 682 helix: 0.79 (0.22), residues: 556 sheet: None (None), residues: 0 loop : 0.63 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 351 TYR 0.020 0.002 TYR B 208 PHE 0.009 0.001 PHE A 212 TRP 0.020 0.002 TRP B 171 HIS 0.007 0.004 HIS B 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 ( 5260) covalent geometry : angle 0.75327 / 0.37 ( 7178) hydrogen bonds : bond 0.04141 / 2.79 ( 428) hydrogen bonds : angle 4.57653 / 3.33 ( 1266) Misc. bond : bond 0.00722 / 0.36 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 LEU cc_start: 0.9326 (mm) cc_final: 0.9096 (mm) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0466 time to fit residues: 3.6321 Evaluate side-chains 47 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.067620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.051897 restraints weight = 19096.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.053267 restraints weight = 13714.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 14)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.054155 restraints weight = 10779.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.054937 restraints weight = 9167.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.055524 restraints weight = 8033.619| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5262 Z= 0.131 Angle : 0.681 7.523 7178 Z= 0.337 Chirality : 0.042 0.174 878 Planarity : 0.004 0.031 894 Dihedral : 6.416 74.857 764 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: 0.89 (0.32), residues: 682 helix: 0.66 (0.22), residues: 562 sheet: None (None), residues: 0 loop : 0.88 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 351 TYR 0.018 0.001 TYR A 208 PHE 0.019 0.001 PHE B 199 TRP 0.004 0.001 TRP B 77 HIS 0.005 0.002 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 ( 5260) covalent geometry : angle 0.68119 / 0.34 ( 7178) hydrogen bonds : bond 0.04011 / 2.74 ( 428) hydrogen bonds : angle 4.46992 / 3.27 ( 1266) Misc. bond : bond 0.00422 / 0.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LEU cc_start: 0.9679 (tp) cc_final: 0.9445 (tp) REVERT: B 111 LEU cc_start: 0.9348 (mm) cc_final: 0.9132 (mm) REVERT: B 212 PHE cc_start: 0.9230 (m-80) cc_final: 0.8929 (m-80) REVERT: B 295 LEU cc_start: 0.9662 (pp) cc_final: 0.9373 (tp) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0547 time to fit residues: 4.0113 Evaluate side-chains 50 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 66 optimal weight: 0.6980 chunk 4 optimal weight: 0.0470 chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 166 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.069356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.052689 restraints weight = 19034.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.053900 restraints weight = 14280.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.054829 restraints weight = 11517.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.055528 restraints weight = 9925.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.056041 restraints weight = 8814.492| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5262 Z= 0.133 Angle : 0.728 9.843 7178 Z= 0.350 Chirality : 0.043 0.231 878 Planarity : 0.004 0.032 894 Dihedral : 6.743 75.934 764 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 0.90 (0.32), residues: 682 helix: 0.65 (0.22), residues: 562 sheet: None (None), residues: 0 loop : 0.98 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 351 TYR 0.015 0.001 TYR A 208 PHE 0.004 0.001 PHE B 187 TRP 0.010 0.002 TRP B 171 HIS 0.005 0.002 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 5260) covalent geometry : angle 0.72789 / 0.35 ( 7178) hydrogen bonds : bond 0.04072 / 2.74 ( 428) hydrogen bonds : angle 4.44084 / 3.27 ( 1266) Misc. bond : bond 0.00399 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LEU cc_start: 0.9674 (tp) cc_final: 0.9429 (tp) REVERT: B 199 PHE cc_start: 0.9396 (t80) cc_final: 0.8833 (t80) REVERT: B 212 PHE cc_start: 0.9198 (m-80) cc_final: 0.8844 (m-80) REVERT: B 270 LEU cc_start: 0.9873 (tt) cc_final: 0.9455 (mt) REVERT: B 295 LEU cc_start: 0.9683 (pp) cc_final: 0.9392 (tp) REVERT: B 344 MET cc_start: 0.9744 (tmm) cc_final: 0.9437 (mmt) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0543 time to fit residues: 4.0331 Evaluate side-chains 44 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.068296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.053379 restraints weight = 22038.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.054679 restraints weight = 15833.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.055699 restraints weight = 12450.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.056435 restraints weight = 10370.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.057003 restraints weight = 9006.004| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5262 Z= 0.129 Angle : 0.673 7.642 7178 Z= 0.333 Chirality : 0.042 0.174 878 Planarity : 0.004 0.031 894 Dihedral : 6.777 82.982 764 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.32), residues: 682 helix: 0.58 (0.21), residues: 574 sheet: None (None), residues: 0 loop : 1.42 (0.61), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 330 TYR 0.012 0.001 TYR B 208 PHE 0.007 0.001 PHE B 199 TRP 0.005 0.001 TRP B 171 HIS 0.007 0.003 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 ( 5260) covalent geometry : angle 0.67290 / 0.33 ( 7178) hydrogen bonds : bond 0.03863 / 2.59 ( 428) hydrogen bonds : angle 4.33954 / 3.18 ( 1266) Misc. bond : bond 0.00217 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LEU cc_start: 0.9657 (tp) cc_final: 0.9421 (tp) REVERT: B 199 PHE cc_start: 0.9369 (t80) cc_final: 0.8580 (t80) REVERT: B 212 PHE cc_start: 0.9190 (m-80) cc_final: 0.8887 (m-80) REVERT: B 270 LEU cc_start: 0.9859 (tt) cc_final: 0.9343 (mt) REVERT: B 293 LEU cc_start: 0.9727 (mm) cc_final: 0.9318 (tp) REVERT: B 295 LEU cc_start: 0.9698 (pp) cc_final: 0.9411 (mt) REVERT: B 344 MET cc_start: 0.9738 (tmm) cc_final: 0.9435 (mmt) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0498 time to fit residues: 3.8449 Evaluate side-chains 49 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 41 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 37 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 165 ASN B 166 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.071753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.051473 restraints weight = 20077.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.052850 restraints weight = 15256.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.053865 restraints weight = 12559.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.054604 restraints weight = 10879.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.055123 restraints weight = 9774.103| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5262 Z= 0.137 Angle : 0.751 10.071 7178 Z= 0.359 Chirality : 0.043 0.212 878 Planarity : 0.004 0.030 894 Dihedral : 6.116 67.583 764 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 0.93 (0.32), residues: 682 helix: 0.61 (0.21), residues: 568 sheet: None (None), residues: 0 loop : 1.41 (0.60), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 351 TYR 0.014 0.001 TYR A 208 PHE 0.006 0.001 PHE A 212 TRP 0.009 0.001 TRP B 171 HIS 0.005 0.002 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 ( 5260) covalent geometry : angle 0.75096 / 0.36 ( 7178) hydrogen bonds : bond 0.03772 / 2.51 ( 428) hydrogen bonds : angle 4.32955 / 3.17 ( 1266) Misc. bond : bond 0.00502 / 0.25 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LEU cc_start: 0.9619 (tp) cc_final: 0.9359 (tp) REVERT: B 199 PHE cc_start: 0.9417 (t80) cc_final: 0.9123 (t80) REVERT: B 212 PHE cc_start: 0.9023 (m-80) cc_final: 0.8807 (m-10) REVERT: B 293 LEU cc_start: 0.9571 (mm) cc_final: 0.9158 (tp) REVERT: B 295 LEU cc_start: 0.9671 (pp) cc_final: 0.9359 (mt) REVERT: B 344 MET cc_start: 0.9768 (tmm) cc_final: 0.9520 (mmt) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0517 time to fit residues: 3.9847 Evaluate side-chains 48 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 60 optimal weight: 0.8980 chunk 6 optimal weight: 0.0670 chunk 51 optimal weight: 0.4980 chunk 18 optimal weight: 0.0970 chunk 54 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 25 optimal weight: 0.0030 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.3126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 135 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.069525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.054050 restraints weight = 22170.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.055325 restraints weight = 16510.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.056306 restraints weight = 13271.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.057043 restraints weight = 11167.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.057601 restraints weight = 9769.186| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.5108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5262 Z= 0.131 Angle : 0.727 12.335 7178 Z= 0.349 Chirality : 0.042 0.127 878 Planarity : 0.004 0.032 894 Dihedral : 6.273 73.317 764 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: 0.86 (0.31), residues: 682 helix: 0.58 (0.21), residues: 570 sheet: None (None), residues: 0 loop : 1.30 (0.58), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 316 TYR 0.011 0.001 TYR B 264 PHE 0.008 0.001 PHE A 334 TRP 0.005 0.001 TRP B 171 HIS 0.005 0.003 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 ( 5260) covalent geometry : angle 0.72687 / 0.35 ( 7178) hydrogen bonds : bond 0.03716 / 2.50 ( 428) hydrogen bonds : angle 4.36292 / 3.20 ( 1266) Misc. bond : bond 0.00016 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 PHE cc_start: 0.9261 (m-80) cc_final: 0.9033 (m-80) REVERT: A 270 LEU cc_start: 0.9865 (tt) cc_final: 0.9473 (mt) REVERT: A 295 LEU cc_start: 0.9720 (pp) cc_final: 0.9447 (mt) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0526 time to fit residues: 4.0450 Evaluate side-chains 51 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 19 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 40 optimal weight: 0.0040 chunk 66 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 0.0020 overall best weight: 0.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.070338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.054523 restraints weight = 21919.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.055780 restraints weight = 16582.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.056699 restraints weight = 13438.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.057416 restraints weight = 11493.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.057892 restraints weight = 10147.664| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5262 Z= 0.141 Angle : 0.778 12.303 7178 Z= 0.376 Chirality : 0.043 0.152 878 Planarity : 0.005 0.036 894 Dihedral : 6.635 74.611 764 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.69 (0.31), residues: 682 helix: 0.48 (0.21), residues: 570 sheet: None (None), residues: 0 loop : 1.14 (0.56), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 215 TYR 0.016 0.001 TYR A 8 PHE 0.006 0.001 PHE A 212 TRP 0.073 0.005 TRP B 171 HIS 0.025 0.011 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 5260) covalent geometry : angle 0.77849 / 0.38 ( 7178) hydrogen bonds : bond 0.03838 / 2.55 ( 428) hydrogen bonds : angle 4.51733 / 3.29 ( 1266) Misc. bond : bond 0.00091 / 0.05 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 TYR cc_start: 0.9063 (m-10) cc_final: 0.8527 (m-10) REVERT: A 212 PHE cc_start: 0.9246 (m-80) cc_final: 0.9015 (m-10) REVERT: A 270 LEU cc_start: 0.9862 (tt) cc_final: 0.9430 (mt) REVERT: A 295 LEU cc_start: 0.9707 (pp) cc_final: 0.9395 (mt) REVERT: A 355 MET cc_start: -0.1160 (ptm) cc_final: -0.1506 (ttm) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0535 time to fit residues: 4.0445 Evaluate side-chains 49 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 0.0170 chunk 7 optimal weight: 0.0370 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 64 optimal weight: 0.2980 chunk 45 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.069865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.054172 restraints weight = 21840.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.055378 restraints weight = 16642.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.056133 restraints weight = 13595.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.056954 restraints weight = 11750.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.057360 restraints weight = 10398.148| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5262 Z= 0.141 Angle : 0.821 11.025 7178 Z= 0.392 Chirality : 0.044 0.239 878 Planarity : 0.004 0.035 894 Dihedral : 5.841 61.925 764 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: 0.69 (0.31), residues: 682 helix: 0.51 (0.21), residues: 570 sheet: None (None), residues: 0 loop : 0.97 (0.54), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 215 TYR 0.015 0.001 TYR A 8 PHE 0.020 0.001 PHE B 128 TRP 0.044 0.003 TRP B 171 HIS 0.007 0.003 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 5260) covalent geometry : angle 0.82118 / 0.39 ( 7178) hydrogen bonds : bond 0.03732 / 2.49 ( 428) hydrogen bonds : angle 4.50330 / 3.28 ( 1266) Misc. bond : bond 0.00469 / 0.24 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 926.68 seconds wall clock time: 16 minutes 44.89 seconds (1004.89 seconds total)