Starting phenix.real_space_refine on Fri Sep 11 00:09:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6hn4_0246/09_2026/6hn4_0246.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hn4_0246/09_2026/6hn4_0246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6hn4_0246/09_2026/6hn4_0246.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6hn4_0246/09_2026/6hn4_0246.cif" model { file = "/net/cci-nas-00/data/ceres_data/6hn4_0246/09_2026/6hn4_0246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hn4_0246/09_2026/6hn4_0246.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hn4_0246/09_2026/6hn4_0246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hn4_0246/09_2026/6hn4_0246.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 48 5.16 5 C 3595 2.51 5 N 981 2.21 5 O 1078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5702 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1629 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Chain: "F" Number of atoms: 3989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3989 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 466} Chain breaks: 4 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.40, per 1000 atoms: 0.25 Number of scatterers: 5702 At special positions: 0 Unit cell: (100.88, 105.04, 102.96, 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 48 16.00 O 1078 8.00 N 981 7.00 C 3595 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS E 647 " - pdb=" SG CYS E 841 " distance=2.04 Simple disulfide: pdb=" SG CYS E 767 " - pdb=" SG CYS E 776 " distance=2.05 Simple disulfide: pdb=" SG CYS F 8 " - pdb=" SG CYS F 26 " distance=2.02 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 155 " distance=2.03 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 182 " distance=2.02 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS F 188 " distance=2.03 Simple disulfide: pdb=" SG CYS F 192 " - pdb=" SG CYS F 201 " distance=2.02 Simple disulfide: pdb=" SG CYS F 196 " - pdb=" SG CYS F 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 208 " - pdb=" SG CYS F 216 " distance=2.03 Simple disulfide: pdb=" SG CYS F 212 " - pdb=" SG CYS F 225 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 237 " distance=2.03 Simple disulfide: pdb=" SG CYS F 241 " - pdb=" SG CYS F 253 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 284 " distance=2.04 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 274 " distance=2.03 Simple disulfide: pdb=" SG CYS F 288 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 304 " - pdb=" SG CYS F 308 " distance=2.04 Simple disulfide: pdb=" SG CYS F 647 " - pdb=" SG CYS F 841 " distance=2.03 Simple disulfide: pdb=" SG CYS F 767 " - pdb=" SG CYS F 776 " distance=2.05 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 Links applied NAG-ASN " NAG F1001 " - " ASN F 16 " " NAG F1002 " - " ASN F 25 " " NAG F1003 " - " ASN F 111 " " NAG F1004 " - " ASN F 606 " " NAG F1005 " - " ASN F 875 " " NAG F1006 " - " ASN F 215 " Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 220.3 milliseconds 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1326 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 16 sheets defined 8.9% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'E' and resid 638 through 644 removed outlier: 4.029A pdb=" N LEU E 644 " --> pdb=" O LEU E 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 844 through 851 Processing helix chain 'F' and resid 17 through 24 Processing helix chain 'F' and resid 42 through 48 removed outlier: 3.801A pdb=" N PHE F 46 " --> pdb=" O ARG F 42 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP F 48 " --> pdb=" O GLU F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 255 through 266 removed outlier: 3.507A pdb=" N CYS F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 644 removed outlier: 4.039A pdb=" N LEU F 644 " --> pdb=" O LEU F 641 " (cutoff:3.500A) Processing helix chain 'F' and resid 844 through 851 Processing sheet with id=AA1, first strand: chain 'E' and resid 599 through 604 removed outlier: 6.521A pdb=" N LYS E 614 " --> pdb=" O PRO E 601 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N SER E 603 " --> pdb=" O ILE E 612 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE E 612 " --> pdb=" O SER E 603 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 740 through 743 Processing sheet with id=AA3, first strand: chain 'E' and resid 800 through 803 Processing sheet with id=AA4, first strand: chain 'E' and resid 841 through 843 removed outlier: 3.660A pdb=" N ALA E 869 " --> pdb=" O GLY E 876 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 841 through 843 Processing sheet with id=AA6, first strand: chain 'F' and resid 6 through 14 removed outlier: 6.557A pdb=" N GLU F 6 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLU F 30 " --> pdb=" O GLU F 6 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS F 8 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N HIS F 32 " --> pdb=" O CYS F 8 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY F 10 " --> pdb=" O HIS F 32 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLN F 34 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP F 12 " --> pdb=" O GLN F 34 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU F 36 " --> pdb=" O ASP F 12 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG F 14 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET F 38 " --> pdb=" O ARG F 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE F 82 " --> pdb=" O ASN F 111 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 6 through 14 removed outlier: 6.557A pdb=" N GLU F 6 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLU F 30 " --> pdb=" O GLU F 6 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS F 8 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N HIS F 32 " --> pdb=" O CYS F 8 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY F 10 " --> pdb=" O HIS F 32 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N GLN F 34 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP F 12 " --> pdb=" O GLN F 34 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU F 36 " --> pdb=" O ASP F 12 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG F 14 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET F 38 " --> pdb=" O ARG F 14 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N LEU F 62 " --> pdb=" O GLY F 31 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU F 33 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N PHE F 64 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE F 35 " --> pdb=" O PHE F 64 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL F 66 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N LEU F 37 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU F 61 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE F 96 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU F 63 " --> pdb=" O PHE F 96 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N TYR F 91 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ARG F 118 " --> pdb=" O TYR F 91 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU F 93 " --> pdb=" O ARG F 118 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N GLU F 120 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE F 95 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL F 117 " --> pdb=" O HIS F 144 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL F 146 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE F 119 " --> pdb=" O VAL F 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 171 through 173 Processing sheet with id=AA9, first strand: chain 'F' and resid 231 through 233 Processing sheet with id=AB1, first strand: chain 'F' and resid 252 through 254 removed outlier: 6.728A pdb=" N HIS F 247 " --> pdb=" O CYS F 284 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 292 through 295 removed outlier: 3.516A pdb=" N LEU F 300 " --> pdb=" O ASN F 295 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 599 through 604 removed outlier: 6.540A pdb=" N LYS F 614 " --> pdb=" O PRO F 601 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N SER F 603 " --> pdb=" O ILE F 612 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE F 612 " --> pdb=" O SER F 603 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 740 through 744 Processing sheet with id=AB5, first strand: chain 'F' and resid 800 through 803 Processing sheet with id=AB6, first strand: chain 'F' and resid 841 through 843 removed outlier: 3.559A pdb=" N ALA F 869 " --> pdb=" O GLY F 876 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 841 through 843 167 hydrogen bonds defined for protein. 387 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: 0.99 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1865 1.35 - 1.48: 1492 1.48 - 1.60: 2430 1.60 - 1.73: 0 1.73 - 1.86: 58 Bond restraints: 5845 Sorted by residual: bond pdb=" C THR F 771 " pdb=" N PRO F 772 " ideal model delta sigma weight residual 1.334 1.427 -0.093 2.34e-02 1.83e+03 1.58e+01 bond pdb=" CA THR F 771 " pdb=" C THR F 771 " ideal model delta sigma weight residual 1.524 1.561 -0.037 1.26e-02 6.30e+03 8.83e+00 bond pdb=" C1 NAG F1005 " pdb=" O5 NAG F1005 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.77e+00 bond pdb=" C1 NAG F1004 " pdb=" O5 NAG F1004 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.57e+00 bond pdb=" N ASN F 90 " pdb=" CA ASN F 90 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.83e-02 2.99e+03 4.35e+00 ... (remaining 5840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.00: 7817 5.00 - 9.99: 110 9.99 - 14.99: 6 14.99 - 19.99: 0 19.99 - 24.99: 2 Bond angle restraints: 7935 Sorted by residual: angle pdb=" C LYS F 197 " pdb=" N SER F 198 " pdb=" CA SER F 198 " ideal model delta sigma weight residual 122.06 109.66 12.40 1.86e+00 2.89e-01 4.45e+01 angle pdb=" C VAL F 99 " pdb=" N HIS F 100 " pdb=" CA HIS F 100 " ideal model delta sigma weight residual 121.54 132.94 -11.40 1.91e+00 2.74e-01 3.56e+01 angle pdb=" N LYS F 197 " pdb=" CA LYS F 197 " pdb=" C LYS F 197 " ideal model delta sigma weight residual 110.80 123.37 -12.57 2.13e+00 2.20e-01 3.48e+01 angle pdb=" CA GLU F 773 " pdb=" CB GLU F 773 " pdb=" CG GLU F 773 " ideal model delta sigma weight residual 114.10 124.68 -10.58 2.00e+00 2.50e-01 2.80e+01 angle pdb=" C PRO E 816 " pdb=" N LYS E 817 " pdb=" CA LYS E 817 " ideal model delta sigma weight residual 121.54 131.28 -9.74 1.91e+00 2.74e-01 2.60e+01 ... (remaining 7930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 3292 14.98 - 29.96: 178 29.96 - 44.94: 33 44.94 - 59.92: 7 59.92 - 74.90: 3 Dihedral angle restraints: 3513 sinusoidal: 1465 harmonic: 2048 Sorted by residual: dihedral pdb=" CB CYS E 647 " pdb=" SG CYS E 647 " pdb=" SG CYS E 841 " pdb=" CB CYS E 841 " ideal model delta sinusoidal sigma weight residual 93.00 164.92 -71.92 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" C THR F 771 " pdb=" N THR F 771 " pdb=" CA THR F 771 " pdb=" CB THR F 771 " ideal model delta harmonic sigma weight residual -122.00 -135.47 13.47 0 2.50e+00 1.60e-01 2.90e+01 dihedral pdb=" SG CYS F 304 " pdb=" CB CYS F 308 " pdb=" SG CYS F 308 " pdb=" CA CYS F 308 " ideal model delta sinusoidal sigma weight residual 79.00 4.10 74.90 1 2.00e+01 2.50e-03 1.77e+01 ... (remaining 3510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 632 0.075 - 0.149: 203 0.149 - 0.224: 34 0.224 - 0.299: 7 0.299 - 0.373: 1 Chirality restraints: 877 Sorted by residual: chirality pdb=" CA THR F 771 " pdb=" N THR F 771 " pdb=" C THR F 771 " pdb=" CB THR F 771 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CB VAL F 146 " pdb=" CA VAL F 146 " pdb=" CG1 VAL F 146 " pdb=" CG2 VAL F 146 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA GLU F 773 " pdb=" N GLU F 773 " pdb=" C GLU F 773 " pdb=" CB GLU F 773 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 874 not shown) Planarity restraints: 1030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU F 818 " -0.016 2.00e-02 2.50e+03 3.13e-02 9.78e+00 pdb=" CD GLU F 818 " 0.054 2.00e-02 2.50e+03 pdb=" OE1 GLU F 818 " -0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU F 818 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 612 " -0.015 2.00e-02 2.50e+03 3.11e-02 9.66e+00 pdb=" C ILE E 612 " 0.054 2.00e-02 2.50e+03 pdb=" O ILE E 612 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU E 613 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 612 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.33e+00 pdb=" C ILE F 612 " -0.053 2.00e-02 2.50e+03 pdb=" O ILE F 612 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU F 613 " 0.017 2.00e-02 2.50e+03 ... (remaining 1027 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 327 2.73 - 3.27: 5041 3.27 - 3.81: 9021 3.81 - 4.36: 10732 4.36 - 4.90: 18402 Nonbonded interactions: 43523 Sorted by model distance: nonbonded pdb=" OH TYR E 781 " pdb=" OH TYR F 67 " model vdw 2.187 3.040 nonbonded pdb=" OG SER F 829 " pdb=" O ARG F 866 " model vdw 2.323 3.040 nonbonded pdb=" OG SER E 829 " pdb=" O ARG E 866 " model vdw 2.339 3.040 nonbonded pdb=" NE2 GLN F 610 " pdb=" OG SER F 752 " model vdw 2.340 3.120 nonbonded pdb=" O SER E 859 " pdb=" OH TYR E 863 " model vdw 2.368 3.040 ... (remaining 43518 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.940 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 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 : 0.007 0.093 5869 Z= 0.321 Angle : 1.515 24.985 7989 Z= 0.826 Chirality : 0.075 0.373 877 Planarity : 0.007 0.031 1024 Dihedral : 9.754 69.511 2133 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 1.75 % Allowed : 6.87 % Favored : 91.37 % Rotamer: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.30), residues: 684 helix: -2.61 (0.76), residues: 28 sheet: -1.98 (0.31), residues: 202 loop : -1.09 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.006 ARG F 866 TYR 0.021 0.004 TYR F 60 PHE 0.039 0.004 PHE F 231 TRP 0.024 0.003 TRP F 878 HIS 0.021 0.002 HIS F 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.32 ( 5845) covalent geometry : angle 1.49713 / 0.82 ( 7935) SS BOND : bond 0.00838 / 0.62 ( 18) SS BOND : angle 3.50355 / 2.44 ( 36) hydrogen bonds : bond 0.14724 / 13.42 ( 147) hydrogen bonds : angle 9.25815 / 6.34 ( 387) link_NAG-ASN : bond 0.00590 / 0.37 ( 6) link_NAG-ASN : angle 2.47728 / 1.74 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.229 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: symmetry clash revert: symmetry clash REVERT: E 740 PHE cc_start: 0.9044 (p90) cc_final: 0.8684 (p90) REVERT: E 741 GLU cc_start: 0.8476 (tp30) cc_final: 0.7662 (tm-30) REVERT: E 747 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8225 (mt-10) REVERT: E 749 LEU cc_start: 0.8725 (tp) cc_final: 0.8499 (tp) REVERT: E 800 THR cc_start: 0.9157 (m) cc_final: 0.8755 (p) REVERT: E 802 GLU cc_start: 0.9339 (mt-10) cc_final: 0.9031 (pt0) REVERT: E 812 MET cc_start: 0.9457 (mtm) cc_final: 0.9028 (mpp) REVERT: E 815 GLU cc_start: 0.9146 (pt0) cc_final: 0.8808 (tm-30) REVERT: E 826 TYR cc_start: 0.8569 (m-80) cc_final: 0.8270 (m-80) REVERT: E 885 TYR cc_start: 0.9234 (t80) cc_final: 0.8973 (t80) REVERT: F 94 VAL cc_start: 0.8798 (t) cc_final: 0.8572 (t) REVERT: F 125 LEU cc_start: 0.9035 (tp) cc_final: 0.8686 (tp) REVERT: F 131 ILE cc_start: 0.8005 (mt) cc_final: 0.7756 (mt) REVERT: F 249 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8403 (tp40) REVERT: F 600 ASP cc_start: 0.8310 (m-30) cc_final: 0.7677 (t0) REVERT: F 629 LEU cc_start: 0.8973 (tp) cc_final: 0.8485 (mt) REVERT: F 757 PHE cc_start: 0.8658 (t80) cc_final: 0.8150 (t80) REVERT: F 787 MET cc_start: 0.8878 (mtt) cc_final: 0.8146 (mtp) REVERT: F 812 MET cc_start: 0.9095 (mtm) cc_final: 0.8653 (mpp) REVERT: F 830 TYR cc_start: 0.8242 (p90) cc_final: 0.7950 (p90) REVERT: F 870 THR cc_start: 0.9273 (m) cc_final: 0.9056 (p) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.0871 time to fit residues: 18.9767 Evaluate side-chains 96 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.0030 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 610 GLN E 635 GLN ** E 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 814 GLN F 15 ASN F 123 ASN F 209 HIS F 610 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.078990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.065012 restraints weight = 26538.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.067068 restraints weight = 15769.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.068504 restraints weight = 10885.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.069542 restraints weight = 8196.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.070289 restraints weight = 6576.203| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5869 Z= 0.159 Angle : 0.768 14.445 7989 Z= 0.382 Chirality : 0.048 0.231 877 Planarity : 0.004 0.037 1024 Dihedral : 5.257 28.186 764 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.16 % Allowed : 2.04 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.90 (0.32), residues: 684 helix: -0.39 (1.04), residues: 28 sheet: -0.88 (0.34), residues: 192 loop : -0.43 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 761 TYR 0.014 0.001 TYR F 60 PHE 0.015 0.002 PHE E 757 TRP 0.012 0.001 TRP E 878 HIS 0.006 0.001 HIS F 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 5845) covalent geometry : angle 0.75723 / 0.38 ( 7935) SS BOND : bond 0.00384 / 0.28 ( 18) SS BOND : angle 1.42249 / 1.25 ( 36) hydrogen bonds : bond 0.04391 / 3.10 ( 147) hydrogen bonds : angle 6.74223 / 4.62 ( 387) link_NAG-ASN : bond 0.00293 / 0.18 ( 6) link_NAG-ASN : angle 2.19557 / 1.61 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.219 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: symmetry clash revert: symmetry clash REVERT: E 740 PHE cc_start: 0.8824 (p90) cc_final: 0.8474 (p90) REVERT: E 826 TYR cc_start: 0.8106 (m-80) cc_final: 0.7816 (m-80) REVERT: F 59 ASP cc_start: 0.7336 (m-30) cc_final: 0.7126 (m-30) REVERT: F 125 LEU cc_start: 0.8597 (tp) cc_final: 0.8132 (tp) REVERT: F 131 ILE cc_start: 0.8280 (mt) cc_final: 0.7922 (mm) REVERT: F 246 TYR cc_start: 0.8601 (m-80) cc_final: 0.8377 (m-80) REVERT: F 641 LEU cc_start: 0.8987 (mp) cc_final: 0.8756 (mt) REVERT: F 757 PHE cc_start: 0.8140 (t80) cc_final: 0.7696 (t80) REVERT: F 787 MET cc_start: 0.9177 (mtt) cc_final: 0.8503 (mtp) REVERT: F 823 ILE cc_start: 0.8178 (mm) cc_final: 0.7621 (mm) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.0913 time to fit residues: 13.2668 Evaluate side-chains 81 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 22 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 814 GLN F 144 HIS F 187 HIS F 218 GLN F 769 GLN F 814 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.074557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.061439 restraints weight = 27968.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.063078 restraints weight = 18163.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.064217 restraints weight = 13239.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.065065 restraints weight = 10490.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.065678 restraints weight = 8742.077| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5869 Z= 0.200 Angle : 0.741 9.942 7989 Z= 0.370 Chirality : 0.048 0.217 877 Planarity : 0.005 0.047 1024 Dihedral : 5.446 31.805 764 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.47 % Allowed : 4.23 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.42 (0.32), residues: 684 helix: -0.28 (0.98), residues: 34 sheet: -0.21 (0.35), residues: 196 loop : -0.24 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 761 TYR 0.014 0.002 TYR F 60 PHE 0.028 0.002 PHE E 884 TRP 0.014 0.001 TRP F 133 HIS 0.011 0.002 HIS E 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 ( 5845) covalent geometry : angle 0.73082 / 0.37 ( 7935) SS BOND : bond 0.00313 / 0.20 ( 18) SS BOND : angle 1.17219 / 0.90 ( 36) hydrogen bonds : bond 0.04051 / 2.90 ( 147) hydrogen bonds : angle 6.30441 / 4.34 ( 387) link_NAG-ASN : bond 0.00247 / 0.16 ( 6) link_NAG-ASN : angle 2.36632 / 1.62 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.139 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: E 740 PHE cc_start: 0.8788 (p90) cc_final: 0.8585 (p90) REVERT: E 800 THR cc_start: 0.8866 (p) cc_final: 0.8616 (p) REVERT: E 812 MET cc_start: 0.8775 (mpp) cc_final: 0.8531 (mpp) REVERT: F 125 LEU cc_start: 0.8249 (tp) cc_final: 0.7859 (tp) REVERT: F 602 ILE cc_start: 0.9110 (mm) cc_final: 0.8087 (pt) REVERT: F 637 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6475 (tm-30) REVERT: F 787 MET cc_start: 0.9298 (mtt) cc_final: 0.8594 (mtp) outliers start: 3 outliers final: 0 residues processed: 96 average time/residue: 0.0773 time to fit residues: 9.7106 Evaluate side-chains 63 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 814 GLN F 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.074970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.061813 restraints weight = 28157.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.063534 restraints weight = 17888.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.064731 restraints weight = 12865.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.065591 restraints weight = 10005.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.066183 restraints weight = 8281.262| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5869 Z= 0.155 Angle : 0.677 9.356 7989 Z= 0.339 Chirality : 0.047 0.223 877 Planarity : 0.004 0.035 1024 Dihedral : 5.265 25.775 764 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.16 % Allowed : 2.98 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.26 (0.32), residues: 684 helix: -0.00 (0.92), residues: 34 sheet: -0.08 (0.35), residues: 200 loop : -0.15 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 761 TYR 0.013 0.001 TYR F 781 PHE 0.025 0.002 PHE E 757 TRP 0.009 0.001 TRP F 133 HIS 0.006 0.001 HIS E 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 5845) covalent geometry : angle 0.66676 / 0.34 ( 7935) SS BOND : bond 0.00265 / 0.18 ( 18) SS BOND : angle 1.18138 / 0.99 ( 36) hydrogen bonds : bond 0.03741 / 2.66 ( 147) hydrogen bonds : angle 6.02133 / 4.20 ( 387) link_NAG-ASN : bond 0.00182 / 0.13 ( 6) link_NAG-ASN : angle 2.13091 / 1.47 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.185 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: F 125 LEU cc_start: 0.8104 (tp) cc_final: 0.7679 (tp) REVERT: F 602 ILE cc_start: 0.9127 (mm) cc_final: 0.8890 (pt) REVERT: F 638 ASP cc_start: 0.8630 (t0) cc_final: 0.8344 (t70) REVERT: F 787 MET cc_start: 0.9300 (mtt) cc_final: 0.8639 (mtp) outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 0.0709 time to fit residues: 8.2490 Evaluate side-chains 57 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 41 optimal weight: 0.0870 chunk 17 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 756 HIS E 814 GLN F 199 HIS F 218 GLN F 610 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.075058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.061793 restraints weight = 28592.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.063465 restraints weight = 18509.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.064620 restraints weight = 13457.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.065457 restraints weight = 10567.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.066100 restraints weight = 8775.657| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5869 Z= 0.128 Angle : 0.638 9.151 7989 Z= 0.320 Chirality : 0.047 0.219 877 Planarity : 0.004 0.036 1024 Dihedral : 5.115 21.533 764 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.16 % Allowed : 1.57 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.12 (0.33), residues: 684 helix: 0.45 (0.92), residues: 34 sheet: -0.02 (0.34), residues: 215 loop : -0.07 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 181 TYR 0.014 0.001 TYR E 826 PHE 0.011 0.001 PHE F 64 TRP 0.008 0.001 TRP E 813 HIS 0.010 0.001 HIS F 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 5845) covalent geometry : angle 0.63002 / 0.32 ( 7935) SS BOND : bond 0.00280 / 0.20 ( 18) SS BOND : angle 0.90660 / 0.73 ( 36) hydrogen bonds : bond 0.03479 / 2.48 ( 147) hydrogen bonds : angle 5.77099 / 4.05 ( 387) link_NAG-ASN : bond 0.00184 / 0.13 ( 6) link_NAG-ASN : angle 2.01259 / 1.39 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.245 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: symmetry clash REVERT: E 740 PHE cc_start: 0.8740 (p90) cc_final: 0.8455 (p90) REVERT: E 800 THR cc_start: 0.8966 (p) cc_final: 0.8718 (p) REVERT: E 812 MET cc_start: 0.8829 (mpp) cc_final: 0.8431 (mpp) REVERT: E 826 TYR cc_start: 0.7891 (m-80) cc_final: 0.7543 (m-80) REVERT: F 38 MET cc_start: 0.7351 (mmt) cc_final: 0.7035 (mmt) REVERT: F 59 ASP cc_start: 0.7515 (m-30) cc_final: 0.7205 (m-30) REVERT: F 125 LEU cc_start: 0.7952 (tp) cc_final: 0.7580 (tp) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.0737 time to fit residues: 8.6163 Evaluate side-chains 66 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.0050 chunk 54 optimal weight: 0.0470 chunk 21 optimal weight: 0.0980 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.2296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 610 GLN E 814 GLN F 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.073893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.060675 restraints weight = 28628.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.062310 restraints weight = 18787.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.063459 restraints weight = 13689.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.064317 restraints weight = 10807.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.064935 restraints weight = 9000.590| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5869 Z= 0.151 Angle : 0.646 9.161 7989 Z= 0.324 Chirality : 0.047 0.215 877 Planarity : 0.004 0.029 1024 Dihedral : 5.126 28.182 764 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.16 % Allowed : 1.25 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.09 (0.33), residues: 684 helix: 0.89 (0.93), residues: 34 sheet: 0.35 (0.36), residues: 201 loop : -0.08 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 181 TYR 0.011 0.001 TYR F 830 PHE 0.014 0.001 PHE E 757 TRP 0.009 0.001 TRP F 133 HIS 0.003 0.001 HIS F 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 5845) covalent geometry : angle 0.63505 / 0.32 ( 7935) SS BOND : bond 0.00284 / 0.19 ( 18) SS BOND : angle 1.15365 / 0.94 ( 36) hydrogen bonds : bond 0.03484 / 2.50 ( 147) hydrogen bonds : angle 5.69191 / 4.00 ( 387) link_NAG-ASN : bond 0.00186 / 0.12 ( 6) link_NAG-ASN : angle 2.16242 / 1.49 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.233 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: E 644 LEU cc_start: 0.8457 (mt) cc_final: 0.7934 (mt) REVERT: E 800 THR cc_start: 0.9000 (p) cc_final: 0.8785 (p) REVERT: E 812 MET cc_start: 0.8859 (mpp) cc_final: 0.8610 (mpp) REVERT: E 826 TYR cc_start: 0.8036 (m-80) cc_final: 0.7636 (m-80) REVERT: F 94 VAL cc_start: 0.9439 (t) cc_final: 0.9215 (p) REVERT: F 125 LEU cc_start: 0.7949 (tp) cc_final: 0.7549 (tp) REVERT: F 638 ASP cc_start: 0.9077 (t0) cc_final: 0.8808 (t70) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.0744 time to fit residues: 8.4317 Evaluate side-chains 62 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 46 optimal weight: 0.0670 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 218 GLN F 814 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.074174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.060936 restraints weight = 28729.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.062598 restraints weight = 18728.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.063776 restraints weight = 13649.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.064643 restraints weight = 10733.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.065294 restraints weight = 8926.056| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5869 Z= 0.126 Angle : 0.607 8.661 7989 Z= 0.306 Chirality : 0.046 0.221 877 Planarity : 0.003 0.026 1024 Dihedral : 4.926 23.455 764 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.16 % Allowed : 1.41 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.11 (0.33), residues: 684 helix: 1.07 (0.94), residues: 34 sheet: 0.29 (0.36), residues: 205 loop : -0.04 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 851 TYR 0.011 0.001 TYR E 826 PHE 0.010 0.001 PHE F 64 TRP 0.007 0.001 TRP E 813 HIS 0.003 0.001 HIS F 846 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 5845) covalent geometry : angle 0.59753 / 0.30 ( 7935) SS BOND : bond 0.00258 / 0.18 ( 18) SS BOND : angle 0.93928 / 0.78 ( 36) hydrogen bonds : bond 0.03333 / 2.36 ( 147) hydrogen bonds : angle 5.43351 / 3.86 ( 387) link_NAG-ASN : bond 0.00179 / 0.12 ( 6) link_NAG-ASN : angle 2.05801 / 1.42 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 644 LEU cc_start: 0.8473 (mt) cc_final: 0.7972 (mt) REVERT: E 826 TYR cc_start: 0.7977 (m-80) cc_final: 0.7728 (m-80) REVERT: F 38 MET cc_start: 0.7524 (mmt) cc_final: 0.7230 (mmp) REVERT: F 59 ASP cc_start: 0.7429 (m-30) cc_final: 0.7146 (m-30) REVERT: F 94 VAL cc_start: 0.9440 (t) cc_final: 0.9220 (p) REVERT: F 125 LEU cc_start: 0.7957 (tp) cc_final: 0.7551 (tp) REVERT: F 246 TYR cc_start: 0.8536 (m-80) cc_final: 0.8003 (m-80) REVERT: F 638 ASP cc_start: 0.9027 (t0) cc_final: 0.8813 (t70) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.0628 time to fit residues: 7.1195 Evaluate side-chains 64 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 814 GLN F 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.071399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.058279 restraints weight = 29184.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.059810 restraints weight = 19286.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.060896 restraints weight = 14258.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.061690 restraints weight = 11356.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.062295 restraints weight = 9556.519| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.6164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 5869 Z= 0.227 Angle : 0.719 9.540 7989 Z= 0.357 Chirality : 0.048 0.226 877 Planarity : 0.004 0.031 1024 Dihedral : 5.353 22.415 764 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.16 % Allowed : 1.57 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.08 (0.33), residues: 684 helix: 1.41 (0.98), residues: 34 sheet: 0.07 (0.36), residues: 206 loop : -0.16 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 851 TYR 0.013 0.002 TYR E 883 PHE 0.013 0.002 PHE E 757 TRP 0.015 0.002 TRP F 133 HIS 0.006 0.001 HIS E 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.23 ( 5845) covalent geometry : angle 0.70654 / 0.35 ( 7935) SS BOND : bond 0.00301 / 0.20 ( 18) SS BOND : angle 1.13533 / 0.83 ( 36) hydrogen bonds : bond 0.03767 / 2.74 ( 147) hydrogen bonds : angle 5.65436 / 4.02 ( 387) link_NAG-ASN : bond 0.00338 / 0.20 ( 6) link_NAG-ASN : angle 2.66839 / 1.82 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 644 LEU cc_start: 0.8570 (mt) cc_final: 0.8068 (mt) REVERT: E 812 MET cc_start: 0.8783 (mpp) cc_final: 0.8550 (mpp) REVERT: E 826 TYR cc_start: 0.7894 (m-80) cc_final: 0.7684 (m-80) REVERT: E 884 PHE cc_start: 0.8131 (m-10) cc_final: 0.7869 (m-10) REVERT: F 94 VAL cc_start: 0.9504 (t) cc_final: 0.9269 (p) REVERT: F 125 LEU cc_start: 0.7926 (tp) cc_final: 0.7604 (tp) REVERT: F 638 ASP cc_start: 0.9045 (t0) cc_final: 0.8837 (t70) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.0633 time to fit residues: 6.6776 Evaluate side-chains 54 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 39 optimal weight: 0.3980 chunk 0 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 123 ASN F 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.073344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.060105 restraints weight = 28793.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.061802 restraints weight = 18454.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.062985 restraints weight = 13286.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.063887 restraints weight = 10396.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.064542 restraints weight = 8583.260| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5869 Z= 0.123 Angle : 0.641 9.154 7989 Z= 0.324 Chirality : 0.047 0.213 877 Planarity : 0.003 0.026 1024 Dihedral : 5.168 25.412 764 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.01 (0.33), residues: 684 helix: 1.32 (0.96), residues: 34 sheet: 0.16 (0.36), residues: 201 loop : -0.13 (0.32), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 851 TYR 0.013 0.001 TYR F 826 PHE 0.015 0.001 PHE E 757 TRP 0.008 0.001 TRP F 133 HIS 0.003 0.001 HIS F 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 5845) covalent geometry : angle 0.63119 / 0.32 ( 7935) SS BOND : bond 0.00267 / 0.19 ( 18) SS BOND : angle 1.08710 / 0.93 ( 36) hydrogen bonds : bond 0.03383 / 2.38 ( 147) hydrogen bonds : angle 5.42774 / 3.90 ( 387) link_NAG-ASN : bond 0.00188 / 0.12 ( 6) link_NAG-ASN : angle 2.15198 / 1.47 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 644 LEU cc_start: 0.8564 (mt) cc_final: 0.8068 (mt) REVERT: E 740 PHE cc_start: 0.8905 (p90) cc_final: 0.8475 (p90) REVERT: F 38 MET cc_start: 0.7517 (mmp) cc_final: 0.7215 (mmp) REVERT: F 94 VAL cc_start: 0.9496 (t) cc_final: 0.9266 (p) REVERT: F 125 LEU cc_start: 0.7821 (tp) cc_final: 0.7476 (tp) REVERT: F 246 TYR cc_start: 0.8520 (m-80) cc_final: 0.8063 (m-80) REVERT: F 638 ASP cc_start: 0.9017 (t0) cc_final: 0.8812 (t70) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0759 time to fit residues: 8.1505 Evaluate side-chains 55 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 chunk 59 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 15 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.074362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.061193 restraints weight = 29392.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.063035 restraints weight = 18442.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.064260 restraints weight = 13078.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.065086 restraints weight = 10114.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.065770 restraints weight = 8410.710| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.6267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5869 Z= 0.110 Angle : 0.636 8.913 7989 Z= 0.319 Chirality : 0.047 0.217 877 Planarity : 0.003 0.026 1024 Dihedral : 5.019 27.136 764 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.04 (0.34), residues: 684 helix: 1.28 (0.96), residues: 34 sheet: 0.23 (0.36), residues: 201 loop : -0.11 (0.32), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 851 TYR 0.008 0.001 TYR E 833 PHE 0.011 0.001 PHE F 64 TRP 0.009 0.001 TRP E 813 HIS 0.009 0.001 HIS F 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 5845) covalent geometry : angle 0.62747 / 0.32 ( 7935) SS BOND : bond 0.00278 / 0.20 ( 18) SS BOND : angle 1.09550 / 0.93 ( 36) hydrogen bonds : bond 0.03149 / 2.20 ( 147) hydrogen bonds : angle 5.35707 / 3.86 ( 387) link_NAG-ASN : bond 0.00198 / 0.13 ( 6) link_NAG-ASN : angle 1.91285 / 1.30 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 644 LEU cc_start: 0.8571 (mt) cc_final: 0.8091 (mt) REVERT: E 740 PHE cc_start: 0.8904 (p90) cc_final: 0.8517 (p90) REVERT: E 812 MET cc_start: 0.8872 (mpp) cc_final: 0.8614 (mpp) REVERT: E 845 LYS cc_start: 0.9404 (tmmt) cc_final: 0.8837 (mtpt) REVERT: F 38 MET cc_start: 0.7478 (mmp) cc_final: 0.7230 (mmp) REVERT: F 94 VAL cc_start: 0.9452 (t) cc_final: 0.9242 (p) REVERT: F 125 LEU cc_start: 0.7873 (tp) cc_final: 0.7560 (tp) REVERT: F 246 TYR cc_start: 0.8460 (m-80) cc_final: 0.8019 (m-80) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0807 time to fit residues: 8.6656 Evaluate side-chains 61 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 0.0870 chunk 53 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.074099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.061143 restraints weight = 28794.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.062908 restraints weight = 18220.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.064127 restraints weight = 12970.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.065031 restraints weight = 10039.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.065667 restraints weight = 8255.629| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.6378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5869 Z= 0.117 Angle : 0.634 9.220 7989 Z= 0.317 Chirality : 0.046 0.219 877 Planarity : 0.003 0.028 1024 Dihedral : 4.968 25.141 764 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.03 (0.34), residues: 684 helix: 0.54 (0.88), residues: 40 sheet: 0.28 (0.36), residues: 201 loop : -0.16 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 851 TYR 0.012 0.001 TYR F 830 PHE 0.011 0.001 PHE F 64 TRP 0.007 0.001 TRP E 813 HIS 0.007 0.001 HIS F 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 5845) covalent geometry : angle 0.62414 / 0.31 ( 7935) SS BOND : bond 0.00221 / 0.16 ( 18) SS BOND : angle 1.10229 / 0.93 ( 36) hydrogen bonds : bond 0.03176 / 2.23 ( 147) hydrogen bonds : angle 5.15589 / 3.72 ( 387) link_NAG-ASN : bond 0.00189 / 0.12 ( 6) link_NAG-ASN : angle 1.99427 / 1.36 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1099.38 seconds wall clock time: 19 minutes 40.69 seconds (1180.69 seconds total)