Starting phenix.real_space_refine on Wed Sep 17 06:08:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hn4_0246/09_2025/6hn4_0246.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hn4_0246/09_2025/6hn4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6hn4_0246/09_2025/6hn4_0246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hn4_0246/09_2025/6hn4_0246.map" model { file = "/net/cci-nas-00/data/ceres_data/6hn4_0246/09_2025/6hn4_0246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hn4_0246/09_2025/6hn4_0246.cif" } 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-2.0-5805/lib/python3.9/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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.51, per 1000 atoms: 0.26 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: 0.37 Conformation dependent library (CDL) restraints added in 179.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.25 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: 0.88 Time building geometry restraints manager: 0.53 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: 3405 14.98 - 29.96: 183 29.96 - 44.94: 41 44.94 - 59.92: 7 59.92 - 74.90: 3 Dihedral angle restraints: 3639 sinusoidal: 1591 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 3636 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.720 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 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 : 9.899 69.511 2259 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 aren 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 covalent geometry : bond 0.00674 ( 5845) covalent geometry : angle 1.49713 ( 7935) SS BOND : bond 0.00838 ( 18) SS BOND : angle 3.50355 ( 36) hydrogen bonds : bond 0.14724 ( 147) hydrogen bonds : angle 9.25815 ( 387) link_NAG-ASN : bond 0.00590 ( 6) link_NAG-ASN : angle 2.47728 ( 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 : 0.150 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: 0.8475 (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: 0.8799 (t) cc_final: 0.8573 (t) REVERT: F 125 LEU cc_start: 0.9035 (tp) cc_final: 0.8685 (tp) REVERT: F 131 ILE cc_start: 0.8005 (mt) cc_final: 0.7755 (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: 0.8877 (mtt) cc_final: 0.8145 (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: 0.0922 time to fit residues: 19.9762 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 : 0.214 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: E 610 GLN E 635 GLN ** E 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 814 GLN F 123 ASN F 209 HIS F 610 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.079035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.065096 restraints weight = 26535.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.067146 restraints weight = 15759.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.068621 restraints weight = 10859.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.069661 restraints weight = 8127.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.070404 restraints weight = 6518.498| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5869 Z= 0.158 Angle : 0.769 14.618 7989 Z= 0.382 Chirality : 0.048 0.225 877 Planarity : 0.004 0.037 1024 Dihedral : 6.232 45.452 890 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 : 2.19 % Favored : 97.65 % 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 aren not related in a simple way. whole: -0.91 (0.32), residues: 684 helix: -0.43 (1.04), residues: 28 sheet: -0.90 (0.34), residues: 192 loop : -0.43 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 761 TYR 0.014 0.001 TYR E 781 PHE 0.013 0.001 PHE E 757 TRP 0.011 0.001 TRP E 878 HIS 0.006 0.001 HIS F 264 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 5845) covalent geometry : angle 0.75859 ( 7935) SS BOND : bond 0.00309 ( 18) SS BOND : angle 1.32323 ( 36) hydrogen bonds : bond 0.04409 ( 147) hydrogen bonds : angle 6.75843 ( 387) link_NAG-ASN : bond 0.00293 ( 6) link_NAG-ASN : angle 2.32603 ( 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 : 0.235 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: 0.8825 (p90) cc_final: 0.8487 (p90) REVERT: E 826 TYR cc_start: 0.8087 (m-80) cc_final: 0.7795 (m-80) REVERT: F 59 ASP cc_start: 0.7339 (m-30) cc_final: 0.7136 (m-30) REVERT: F 125 LEU cc_start: 0.8590 (tp) cc_final: 0.8104 (tp) REVERT: F 131 ILE cc_start: 0.8279 (mt) cc_final: 0.7923 (mm) REVERT: F 246 TYR cc_start: 0.8590 (m-80) cc_final: 0.8367 (m-80) REVERT: F 641 LEU cc_start: 0.8986 (mp) cc_final: 0.8755 (mt) REVERT: F 757 PHE cc_start: 0.8122 (t80) cc_final: 0.7681 (t80) REVERT: F 787 MET cc_start: 0.9180 (mtt) cc_final: 0.8508 (mtp) REVERT: F 823 ILE cc_start: 0.8177 (mm) cc_final: 0.7621 (mm) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.0948 time to fit residues: 13.7475 Evaluate side-chains 78 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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: 6.9990 chunk 36 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 34 optimal weight: 0.0470 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 814 GLN F 15 ASN F 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.076715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.063399 restraints weight = 27347.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.065222 restraints weight = 17149.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.066469 restraints weight = 12208.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.067355 restraints weight = 9450.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.068018 restraints weight = 7796.543| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5869 Z= 0.153 Angle : 0.708 9.250 7989 Z= 0.354 Chirality : 0.048 0.216 877 Planarity : 0.005 0.053 1024 Dihedral : 6.093 43.344 890 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.16 % Allowed : 3.29 % Favored : 96.55 % 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 aren not related in a simple way. whole: -0.41 (0.32), residues: 684 helix: -0.20 (0.99), residues: 34 sheet: -0.22 (0.36), residues: 186 loop : -0.25 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 761 TYR 0.011 0.001 TYR F 60 PHE 0.021 0.002 PHE E 884 TRP 0.009 0.001 TRP F 133 HIS 0.006 0.001 HIS F 264 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5845) covalent geometry : angle 0.69857 ( 7935) SS BOND : bond 0.00405 ( 18) SS BOND : angle 1.07835 ( 36) hydrogen bonds : bond 0.03914 ( 147) hydrogen bonds : angle 6.24313 ( 387) link_NAG-ASN : bond 0.00250 ( 6) link_NAG-ASN : angle 2.21192 ( 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 92 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.157 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: E 740 PHE cc_start: 0.8742 (p90) cc_final: 0.8480 (p90) REVERT: E 800 THR cc_start: 0.8846 (p) cc_final: 0.8640 (p) REVERT: E 812 MET cc_start: 0.8720 (mpp) cc_final: 0.8454 (mpp) REVERT: F 102 LYS cc_start: 0.8410 (pttm) cc_final: 0.8195 (mmmm) REVERT: F 125 LEU cc_start: 0.8338 (tp) cc_final: 0.7878 (tp) REVERT: F 637 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6545 (tm-30) REVERT: F 787 MET cc_start: 0.9285 (mtt) cc_final: 0.8667 (mtp) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.0817 time to fit residues: 9.6996 Evaluate side-chains 67 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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: 3.9990 chunk 46 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 chunk 55 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 814 GLN E 839 HIS F 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.077594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.064337 restraints weight = 27617.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.066185 restraints weight = 17548.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.067440 restraints weight = 12477.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.068341 restraints weight = 9660.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.068983 restraints weight = 7957.792| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5869 Z= 0.119 Angle : 0.647 8.389 7989 Z= 0.323 Chirality : 0.047 0.230 877 Planarity : 0.004 0.035 1024 Dihedral : 5.650 40.537 890 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.16 % Allowed : 2.51 % Favored : 97.34 % 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 aren not related in a simple way. whole: -0.14 (0.33), residues: 684 helix: -0.34 (0.91), residues: 34 sheet: 0.17 (0.37), residues: 194 loop : -0.13 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 761 TYR 0.018 0.001 TYR F 781 PHE 0.013 0.001 PHE F 64 TRP 0.007 0.001 TRP E 632 HIS 0.005 0.001 HIS F 839 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 5845) covalent geometry : angle 0.63796 ( 7935) SS BOND : bond 0.00241 ( 18) SS BOND : angle 1.12408 ( 36) hydrogen bonds : bond 0.03598 ( 147) hydrogen bonds : angle 5.93046 ( 387) link_NAG-ASN : bond 0.00267 ( 6) link_NAG-ASN : angle 2.00595 ( 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 94 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.203 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: 0.8724 (p90) cc_final: 0.8373 (p90) REVERT: E 812 MET cc_start: 0.8790 (mpp) cc_final: 0.8568 (mpp) REVERT: F 59 ASP cc_start: 0.7564 (m-30) cc_final: 0.7305 (m-30) REVERT: F 125 LEU cc_start: 0.8329 (tp) cc_final: 0.7879 (tp) REVERT: F 787 MET cc_start: 0.9251 (mtt) cc_final: 0.8667 (mtp) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.0753 time to fit residues: 9.4777 Evaluate side-chains 65 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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: 0.7980 chunk 63 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 42 optimal weight: 0.0370 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 814 GLN F 108 ASN F 218 GLN F 610 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 = 0.3748 r_free = 0.3748 target = 0.075976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.062402 restraints weight = 28161.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.064198 restraints weight = 17937.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.065480 restraints weight = 12836.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.066345 restraints weight = 9969.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.067019 restraints weight = 8239.141| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4824 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= 0.141 Angle : 0.637 8.177 7989 Z= 0.319 Chirality : 0.047 0.218 877 Planarity : 0.004 0.032 1024 Dihedral : 5.257 29.098 890 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.31 % Allowed : 1.72 % Favored : 97.96 % 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 aren not related in a simple way. whole: 0.04 (0.33), residues: 684 helix: 0.16 (0.90), residues: 34 sheet: 0.35 (0.37), residues: 196 loop : -0.07 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 181 TYR 0.010 0.001 TYR F 60 PHE 0.019 0.001 PHE E 884 TRP 0.008 0.001 TRP F 133 HIS 0.004 0.001 HIS E 801 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5845) covalent geometry : angle 0.62709 ( 7935) SS BOND : bond 0.00271 ( 18) SS BOND : angle 0.90989 ( 36) hydrogen bonds : bond 0.03568 ( 147) hydrogen bonds : angle 5.69742 ( 387) link_NAG-ASN : bond 0.00209 ( 6) link_NAG-ASN : angle 2.25251 ( 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 87 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.238 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: 0.8267 (tp) cc_final: 0.7832 (tp) REVERT: F 787 MET cc_start: 0.9304 (mtt) cc_final: 0.8696 (mtp) outliers start: 2 outliers final: 0 residues processed: 87 average time/residue: 0.0813 time to fit residues: 9.3812 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 : 0.244 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 21 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 610 GLN ** E 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3720 r_free = 0.3720 target = 0.074562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.061325 restraints weight = 28474.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.062951 restraints weight = 18851.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.064107 restraints weight = 13736.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.064918 restraints weight = 10835.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.065561 restraints weight = 9061.408| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5869 Z= 0.158 Angle : 0.656 8.523 7989 Z= 0.329 Chirality : 0.047 0.220 877 Planarity : 0.004 0.027 1024 Dihedral : 5.145 28.922 890 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.16 % Allowed : 1.72 % Favored : 98.12 % 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 aren not related in a simple way. whole: 0.12 (0.33), residues: 684 helix: 0.71 (0.92), residues: 34 sheet: 0.37 (0.36), residues: 206 loop : -0.04 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 181 TYR 0.011 0.001 TYR F 60 PHE 0.011 0.001 PHE F 64 TRP 0.011 0.001 TRP F 133 HIS 0.004 0.001 HIS F 839 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 5845) covalent geometry : angle 0.64351 ( 7935) SS BOND : bond 0.00431 ( 18) SS BOND : angle 1.16635 ( 36) hydrogen bonds : bond 0.03480 ( 147) hydrogen bonds : angle 5.63407 ( 387) link_NAG-ASN : bond 0.00223 ( 6) link_NAG-ASN : angle 2.39518 ( 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 : 0.162 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: 0.8403 (mt) cc_final: 0.7840 (tt) REVERT: F 38 MET cc_start: 0.7461 (mmt) cc_final: 0.7178 (mmp) REVERT: F 94 VAL cc_start: 0.9404 (t) cc_final: 0.9180 (p) REVERT: F 125 LEU cc_start: 0.7819 (tp) cc_final: 0.7457 (tp) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.0817 time to fit residues: 9.1775 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 : 0.148 ------------------------------------------------------------------------------- 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: 0.8980 chunk 37 optimal weight: 0.3980 chunk 66 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.074832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.061508 restraints weight = 28244.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.063201 restraints weight = 18418.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.064428 restraints weight = 13285.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.065276 restraints weight = 10362.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.065936 restraints weight = 8597.919| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.5450 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 : 0.628 8.309 7989 Z= 0.316 Chirality : 0.047 0.221 877 Planarity : 0.003 0.027 1024 Dihedral : 5.003 25.347 890 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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 aren not related in a simple way. whole: 0.14 (0.33), residues: 684 helix: 1.16 (0.95), residues: 34 sheet: 0.37 (0.36), residues: 211 loop : -0.07 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 851 TYR 0.010 0.001 TYR F 60 PHE 0.015 0.001 PHE F 642 TRP 0.008 0.001 TRP F 133 HIS 0.013 0.001 HIS F 199 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 5845) covalent geometry : angle 0.61797 ( 7935) SS BOND : bond 0.00249 ( 18) SS BOND : angle 0.95546 ( 36) hydrogen bonds : bond 0.03327 ( 147) hydrogen bonds : angle 5.53952 ( 387) link_NAG-ASN : bond 0.00201 ( 6) link_NAG-ASN : angle 2.26768 ( 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 86 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 644 LEU cc_start: 0.8410 (mt) cc_final: 0.7928 (mt) REVERT: F 38 MET cc_start: 0.7546 (mmt) cc_final: 0.7164 (mmp) REVERT: F 94 VAL cc_start: 0.9422 (t) cc_final: 0.9212 (p) REVERT: F 125 LEU cc_start: 0.7819 (tp) cc_final: 0.7428 (tp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0828 time to fit residues: 9.1743 Evaluate side-chains 58 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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: 4.9990 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 814 GLN F 108 ASN F 218 GLN F 814 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.073984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.060827 restraints weight = 28195.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.062479 restraints weight = 18520.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.063606 restraints weight = 13576.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.064364 restraints weight = 10731.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.065068 restraints weight = 9040.885| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5747 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= 0.139 Angle : 0.631 8.621 7989 Z= 0.315 Chirality : 0.046 0.223 877 Planarity : 0.004 0.033 1024 Dihedral : 4.848 21.927 890 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.31 % Allowed : 0.63 % Favored : 99.06 % 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 aren not related in a simple way. whole: 0.11 (0.33), residues: 684 helix: 0.56 (0.90), residues: 40 sheet: 0.48 (0.36), residues: 211 loop : -0.12 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 851 TYR 0.010 0.001 TYR F 60 PHE 0.009 0.001 PHE F 231 TRP 0.009 0.001 TRP E 813 HIS 0.006 0.001 HIS F 839 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 5845) covalent geometry : angle 0.62057 ( 7935) SS BOND : bond 0.00211 ( 18) SS BOND : angle 0.95351 ( 36) hydrogen bonds : bond 0.03306 ( 147) hydrogen bonds : angle 5.40323 ( 387) link_NAG-ASN : bond 0.00200 ( 6) link_NAG-ASN : angle 2.31013 ( 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 83 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 644 LEU cc_start: 0.8488 (mt) cc_final: 0.7999 (mt) REVERT: F 38 MET cc_start: 0.7583 (mmt) cc_final: 0.7269 (mmp) REVERT: F 94 VAL cc_start: 0.9433 (t) cc_final: 0.9222 (p) REVERT: F 125 LEU cc_start: 0.7902 (tp) cc_final: 0.7542 (tp) REVERT: F 246 TYR cc_start: 0.8520 (m-80) cc_final: 0.7962 (m-80) outliers start: 2 outliers final: 0 residues processed: 83 average time/residue: 0.0816 time to fit residues: 8.8604 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 : 0.189 ------------------------------------------------------------------------------- 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: 4.9990 chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 0 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.072488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.059383 restraints weight = 28900.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.060950 restraints weight = 19351.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.062044 restraints weight = 14251.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.062866 restraints weight = 11303.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.063460 restraints weight = 9459.681| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5869 Z= 0.184 Angle : 0.676 8.861 7989 Z= 0.340 Chirality : 0.047 0.216 877 Planarity : 0.004 0.026 1024 Dihedral : 5.121 26.473 890 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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 aren not related in a simple way. whole: 0.02 (0.33), residues: 684 helix: 1.43 (0.99), residues: 34 sheet: 0.49 (0.36), residues: 200 loop : -0.28 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 851 TYR 0.011 0.001 TYR F 60 PHE 0.010 0.001 PHE F 231 TRP 0.014 0.001 TRP F 133 HIS 0.007 0.001 HIS E 846 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 5845) covalent geometry : angle 0.66253 ( 7935) SS BOND : bond 0.00271 ( 18) SS BOND : angle 1.19180 ( 36) hydrogen bonds : bond 0.03473 ( 147) hydrogen bonds : angle 5.40341 ( 387) link_NAG-ASN : bond 0.00249 ( 6) link_NAG-ASN : angle 2.57394 ( 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 79 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 644 LEU cc_start: 0.8486 (mt) cc_final: 0.8076 (mt) REVERT: E 884 PHE cc_start: 0.8091 (m-10) cc_final: 0.7758 (m-10) REVERT: F 94 VAL cc_start: 0.9446 (t) cc_final: 0.9232 (p) REVERT: F 125 LEU cc_start: 0.7831 (tp) cc_final: 0.7496 (tp) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0969 time to fit residues: 9.8674 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 : 0.206 ------------------------------------------------------------------------------- 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: 6.9990 chunk 20 optimal weight: 0.0270 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 60 optimal weight: 0.0060 chunk 47 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.074551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.061284 restraints weight = 28857.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.062957 restraints weight = 19039.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.064165 restraints weight = 13804.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.065053 restraints weight = 10807.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.065706 restraints weight = 8949.083| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.6136 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= 0.115 Angle : 0.633 8.530 7989 Z= 0.317 Chirality : 0.047 0.219 877 Planarity : 0.003 0.027 1024 Dihedral : 4.963 27.762 890 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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 aren not related in a simple way. whole: -0.01 (0.33), residues: 684 helix: 0.60 (0.92), residues: 40 sheet: 0.42 (0.37), residues: 201 loop : -0.22 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 851 TYR 0.012 0.001 TYR F 246 PHE 0.009 0.001 PHE F 231 TRP 0.009 0.001 TRP E 813 HIS 0.004 0.001 HIS F 199 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 5845) covalent geometry : angle 0.62277 ( 7935) SS BOND : bond 0.00230 ( 18) SS BOND : angle 1.13327 ( 36) hydrogen bonds : bond 0.03259 ( 147) hydrogen bonds : angle 5.19015 ( 387) link_NAG-ASN : bond 0.00201 ( 6) link_NAG-ASN : angle 2.11414 ( 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 85 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 644 LEU cc_start: 0.8531 (mt) cc_final: 0.8085 (mt) REVERT: E 845 LYS cc_start: 0.9411 (tmmt) cc_final: 0.8816 (mtpt) REVERT: E 884 PHE cc_start: 0.8049 (m-10) cc_final: 0.7667 (m-10) REVERT: F 38 MET cc_start: 0.7517 (mmp) cc_final: 0.7266 (mmp) REVERT: F 94 VAL cc_start: 0.9444 (t) cc_final: 0.9235 (p) REVERT: F 125 LEU cc_start: 0.7839 (tp) cc_final: 0.7510 (tp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0877 time to fit residues: 9.5817 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 : 0.231 ------------------------------------------------------------------------------- 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: 2.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 0.0970 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 HIS F 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.074352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.061304 restraints weight = 28513.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.063083 restraints weight = 18268.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.064264 restraints weight = 13067.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.065120 restraints weight = 10175.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.065773 restraints weight = 8411.877| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.6235 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= 0.123 Angle : 0.636 8.392 7989 Z= 0.320 Chirality : 0.046 0.223 877 Planarity : 0.003 0.024 1024 Dihedral : 4.851 26.230 890 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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 aren not related in a simple way. whole: 0.02 (0.33), residues: 684 helix: 0.51 (0.88), residues: 40 sheet: 0.47 (0.37), residues: 201 loop : -0.20 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 851 TYR 0.008 0.001 TYR F 246 PHE 0.011 0.001 PHE F 64 TRP 0.009 0.001 TRP E 813 HIS 0.004 0.001 HIS F 199 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 5845) covalent geometry : angle 0.62509 ( 7935) SS BOND : bond 0.00220 ( 18) SS BOND : angle 1.11122 ( 36) hydrogen bonds : bond 0.03241 ( 147) hydrogen bonds : angle 5.20767 ( 387) link_NAG-ASN : bond 0.00217 ( 6) link_NAG-ASN : angle 2.16142 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1129.80 seconds wall clock time: 20 minutes 8.31 seconds (1208.31 seconds total)