Starting phenix.real_space_refine on Thu Mar 6 10:34:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hn4_0246/03_2025/6hn4_0246.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hn4_0246/03_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_0246/03_2025/6hn4_0246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hn4_0246/03_2025/6hn4_0246.map" model { file = "/net/cci-nas-00/data/ceres_data/6hn4_0246/03_2025/6hn4_0246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hn4_0246/03_2025/6hn4_0246.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.51, per 1000 atoms: 0.79 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: 1.94 Conformation dependent library (CDL) restraints added in 819.6 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: 0.75 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: 2.05 Time building geometry restraints manager: 2.20 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: 1.660 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 19.750 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.070 ------------------------------------------------------------------------------- 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 5845 Z= 0.456 Angle : 1.497 24.985 7935 Z= 0.820 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.003 TRP F 878 HIS 0.021 0.002 HIS F 32 PHE 0.039 0.004 PHE F 231 TYR 0.021 0.004 TYR F 60 ARG 0.037 0.006 ARG F 866 *********************** 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 : 0.659 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 600 ASP cc_start: 0.8950 (m-30) cc_final: 0.8727 (t0) REVERT: E 740 PHE cc_start: 0.9044 (p90) cc_final: 0.8685 (p90) REVERT: E 741 GLU cc_start: 0.8475 (tp30) cc_final: 0.7661 (tm-30) REVERT: E 747 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8524 (mt-10) REVERT: E 749 LEU cc_start: 0.8725 (tp) cc_final: 0.8498 (tp) REVERT: E 800 THR cc_start: 0.9157 (m) cc_final: 0.8753 (p) REVERT: E 802 GLU cc_start: 0.9339 (mt-10) cc_final: 0.9055 (pt0) REVERT: E 812 MET cc_start: 0.9457 (mtm) cc_final: 0.9029 (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: 0.8686 (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: 0.8474 (mt) REVERT: F 757 PHE cc_start: 0.8658 (t80) cc_final: 0.8358 (t80) REVERT: F 787 MET cc_start: 0.8877 (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: 0.9057 (p) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2787 time to fit residues: 60.1042 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 : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 15 ASN F 123 ASN F 187 HIS 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 = 0.3767 r_free = 0.3767 target = 0.077378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.063753 restraints weight = 26951.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.065562 restraints weight = 16883.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.066861 restraints weight = 11995.692| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5845 Z= 0.292 Angle : 0.776 13.641 7935 Z= 0.386 Chirality : 0.048 0.245 877 Planarity : 0.004 0.035 1024 Dihedral : 6.281 43.845 890 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.32), residues: 684 helix: -0.53 (1.02), residues: 28 sheet: -0.93 (0.34), residues: 188 loop : -0.37 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 133 HIS 0.006 0.001 HIS F 264 PHE 0.012 0.002 PHE F 64 TYR 0.017 0.002 TYR E 628 ARG 0.007 0.001 ARG E 761 *********************** 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 111 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.791 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: 0.8798 (p90) cc_final: 0.8582 (p90) REVERT: E 826 TYR cc_start: 0.8067 (m-80) cc_final: 0.7845 (m-80) REVERT: F 125 LEU cc_start: 0.8523 (tp) cc_final: 0.8115 (tp) REVERT: F 246 TYR cc_start: 0.8633 (m-80) cc_final: 0.8415 (m-80) REVERT: F 641 LEU cc_start: 0.9016 (mp) cc_final: 0.8752 (mt) REVERT: F 757 PHE cc_start: 0.8208 (t80) cc_final: 0.7803 (t80) REVERT: F 787 MET cc_start: 0.9218 (mtt) cc_final: 0.8554 (mtp) REVERT: F 823 ILE cc_start: 0.8295 (mm) cc_final: 0.7808 (mm) REVERT: F 870 THR cc_start: 0.9294 (m) cc_final: 0.9083 (p) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.2920 time to fit residues: 39.8309 Evaluate side-chains 74 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 52 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 765 GLN E 814 GLN F 144 HIS F 218 GLN F 610 GLN F 769 GLN F 814 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.072013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.058774 restraints weight = 28987.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.060387 restraints weight = 18489.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.061528 restraints weight = 13327.574| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 5845 Z= 0.406 Angle : 0.822 11.206 7935 Z= 0.415 Chirality : 0.049 0.169 877 Planarity : 0.005 0.044 1024 Dihedral : 6.492 46.229 890 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.31 % Allowed : 4.23 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.32), residues: 684 helix: 0.00 (1.05), residues: 28 sheet: -0.44 (0.35), residues: 195 loop : -0.28 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 133 HIS 0.008 0.002 HIS F 185 PHE 0.032 0.002 PHE E 884 TYR 0.016 0.002 TYR F 60 ARG 0.014 0.001 ARG E 831 *********************** 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 87 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 800 THR cc_start: 0.8905 (p) cc_final: 0.8688 (p) REVERT: E 817 LYS cc_start: 0.8744 (pttp) cc_final: 0.8531 (mmmt) REVERT: F 94 VAL cc_start: 0.9482 (t) cc_final: 0.9237 (p) REVERT: F 125 LEU cc_start: 0.8124 (tp) cc_final: 0.7841 (tp) REVERT: F 600 ASP cc_start: 0.8215 (t0) cc_final: 0.7822 (t0) REVERT: F 638 ASP cc_start: 0.8552 (m-30) cc_final: 0.8260 (t70) REVERT: F 787 MET cc_start: 0.9303 (mtt) cc_final: 0.8618 (mtp) outliers start: 2 outliers final: 0 residues processed: 87 average time/residue: 0.2011 time to fit residues: 23.1868 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 : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 10 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 0 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 610 GLN E 814 GLN 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 = 0.3676 r_free = 0.3676 target = 0.072514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.059354 restraints weight = 29336.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.061010 restraints weight = 18505.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.062198 restraints weight = 13227.463| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5845 Z= 0.279 Angle : 0.703 9.692 7935 Z= 0.355 Chirality : 0.047 0.227 877 Planarity : 0.004 0.030 1024 Dihedral : 5.981 45.730 890 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.31 % Allowed : 2.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.32), residues: 684 helix: 0.06 (0.89), residues: 34 sheet: -0.42 (0.36), residues: 199 loop : -0.17 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 133 HIS 0.004 0.001 HIS F 185 PHE 0.017 0.002 PHE F 64 TYR 0.011 0.002 TYR E 826 ARG 0.004 0.001 ARG F 844 *********************** 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 82 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 812 MET cc_start: 0.8805 (mpp) cc_final: 0.8525 (mpp) REVERT: F 94 VAL cc_start: 0.9462 (t) cc_final: 0.9224 (p) REVERT: F 125 LEU cc_start: 0.7943 (tp) cc_final: 0.7619 (tp) REVERT: F 638 ASP cc_start: 0.8541 (m-30) cc_final: 0.8231 (t70) outliers start: 2 outliers final: 0 residues processed: 82 average time/residue: 0.1591 time to fit residues: 17.7882 Evaluate side-chains 49 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 57 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 814 GLN ** F 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 GLN ** F 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.072255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.059296 restraints weight = 28974.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.060896 restraints weight = 18564.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.062035 restraints weight = 13494.202| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5845 Z= 0.260 Angle : 0.667 9.940 7935 Z= 0.337 Chirality : 0.047 0.218 877 Planarity : 0.004 0.029 1024 Dihedral : 5.567 42.523 890 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.16 % Allowed : 1.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.32), residues: 684 helix: 0.73 (0.94), residues: 34 sheet: -0.20 (0.36), residues: 195 loop : -0.17 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 133 HIS 0.015 0.001 HIS F 199 PHE 0.015 0.002 PHE E 884 TYR 0.011 0.001 TYR F 60 ARG 0.008 0.001 ARG E 854 *********************** 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 75 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 812 MET cc_start: 0.8813 (mpp) cc_final: 0.8542 (mpp) REVERT: E 826 TYR cc_start: 0.8315 (m-10) cc_final: 0.8059 (m-80) REVERT: F 94 VAL cc_start: 0.9453 (t) cc_final: 0.9213 (p) REVERT: F 125 LEU cc_start: 0.7776 (tp) cc_final: 0.7476 (tp) REVERT: F 638 ASP cc_start: 0.8571 (m-30) cc_final: 0.8276 (t70) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.1722 time to fit residues: 17.3146 Evaluate side-chains 51 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 46 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 814 GLN F 218 GLN F 814 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.070316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.057536 restraints weight = 29690.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.059070 restraints weight = 19344.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.060153 restraints weight = 14149.140| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.6117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 5845 Z= 0.314 Angle : 0.701 10.292 7935 Z= 0.354 Chirality : 0.048 0.230 877 Planarity : 0.004 0.030 1024 Dihedral : 5.520 38.918 890 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.31 % Allowed : 2.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.33), residues: 684 helix: 0.11 (0.92), residues: 42 sheet: -0.31 (0.35), residues: 202 loop : -0.25 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 133 HIS 0.006 0.002 HIS F 839 PHE 0.013 0.002 PHE E 757 TYR 0.017 0.002 TYR E 883 ARG 0.004 0.001 ARG F 181 *********************** 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 76 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 826 TYR cc_start: 0.8327 (m-10) cc_final: 0.8088 (m-80) REVERT: F 125 LEU cc_start: 0.7805 (tp) cc_final: 0.7547 (tp) REVERT: F 246 TYR cc_start: 0.8584 (m-80) cc_final: 0.8050 (m-80) REVERT: F 600 ASP cc_start: 0.8375 (t70) cc_final: 0.8166 (t0) REVERT: F 638 ASP cc_start: 0.8620 (m-30) cc_final: 0.8376 (t70) REVERT: F 787 MET cc_start: 0.9267 (mtt) cc_final: 0.8630 (mtt) REVERT: F 838 LEU cc_start: 0.8673 (mp) cc_final: 0.8387 (tp) outliers start: 2 outliers final: 0 residues processed: 76 average time/residue: 0.1889 time to fit residues: 19.0396 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 : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 52 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 F 801 HIS ** F 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.069160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.057595 restraints weight = 30660.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.058964 restraints weight = 17234.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.060299 restraints weight = 12633.713| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.6557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 5845 Z= 0.379 Angle : 0.745 10.241 7935 Z= 0.375 Chirality : 0.049 0.214 877 Planarity : 0.005 0.040 1024 Dihedral : 5.845 38.747 890 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.33), residues: 684 helix: -0.29 (0.84), residues: 48 sheet: -0.42 (0.35), residues: 214 loop : -0.42 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 133 HIS 0.007 0.002 HIS F 199 PHE 0.017 0.002 PHE E 757 TYR 0.018 0.002 TYR E 883 ARG 0.004 0.001 ARG F 181 *********************** 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 73 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 826 TYR cc_start: 0.8250 (m-10) cc_final: 0.8006 (m-80) REVERT: E 845 LYS cc_start: 0.9410 (tmmt) cc_final: 0.8963 (mttt) REVERT: F 246 TYR cc_start: 0.8548 (m-80) cc_final: 0.8162 (m-80) REVERT: F 600 ASP cc_start: 0.8232 (t70) cc_final: 0.8026 (t0) REVERT: F 638 ASP cc_start: 0.8683 (m-30) cc_final: 0.8428 (t70) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1907 time to fit residues: 18.4354 Evaluate side-chains 52 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 16 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 814 GLN F 123 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 = 0.3646 r_free = 0.3646 target = 0.070932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.058085 restraints weight = 29144.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.059644 restraints weight = 18887.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.060773 restraints weight = 13802.552| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.6633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5845 Z= 0.243 Angle : 0.654 7.648 7935 Z= 0.333 Chirality : 0.047 0.226 877 Planarity : 0.004 0.031 1024 Dihedral : 5.576 34.678 890 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.31 % Allowed : 0.78 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.33), residues: 684 helix: 0.36 (0.87), residues: 40 sheet: -0.31 (0.35), residues: 212 loop : -0.31 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 615 HIS 0.005 0.001 HIS F 839 PHE 0.013 0.001 PHE E 757 TYR 0.010 0.001 TYR F 127 ARG 0.011 0.000 ARG F 851 *********************** 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 81 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 826 TYR cc_start: 0.8312 (m-10) cc_final: 0.8047 (m-80) REVERT: E 845 LYS cc_start: 0.9392 (tmmt) cc_final: 0.9035 (mttt) REVERT: F 94 VAL cc_start: 0.9500 (t) cc_final: 0.9261 (p) REVERT: F 125 LEU cc_start: 0.8552 (tp) cc_final: 0.8324 (tp) REVERT: F 246 TYR cc_start: 0.8524 (m-80) cc_final: 0.8119 (m-80) REVERT: F 828 VAL cc_start: 0.9439 (t) cc_final: 0.9035 (t) REVERT: F 830 TYR cc_start: 0.8483 (p90) cc_final: 0.8270 (p90) REVERT: F 838 LEU cc_start: 0.8875 (mp) cc_final: 0.8513 (tp) outliers start: 2 outliers final: 0 residues processed: 81 average time/residue: 0.1825 time to fit residues: 19.7106 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 : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 4 optimal weight: 0.0050 chunk 8 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3667 r_free = 0.3667 target = 0.071964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.059278 restraints weight = 29089.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.060877 restraints weight = 18953.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.061998 restraints weight = 13793.873| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.6646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5845 Z= 0.190 Angle : 0.637 10.974 7935 Z= 0.322 Chirality : 0.047 0.227 877 Planarity : 0.004 0.032 1024 Dihedral : 5.194 29.292 890 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.33), residues: 684 helix: 0.31 (0.88), residues: 40 sheet: -0.06 (0.35), residues: 206 loop : -0.34 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 878 HIS 0.004 0.001 HIS F 839 PHE 0.014 0.001 PHE E 757 TYR 0.009 0.001 TYR F 826 ARG 0.011 0.000 ARG F 851 *********************** 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 : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 826 TYR cc_start: 0.8328 (m-10) cc_final: 0.8090 (m-80) REVERT: E 845 LYS cc_start: 0.9374 (tmmt) cc_final: 0.9019 (mtpt) REVERT: F 94 VAL cc_start: 0.9482 (t) cc_final: 0.9249 (p) REVERT: F 125 LEU cc_start: 0.8409 (tp) cc_final: 0.8131 (tp) REVERT: F 246 TYR cc_start: 0.8526 (m-80) cc_final: 0.8118 (m-80) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1791 time to fit residues: 19.3396 Evaluate side-chains 56 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 41 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 0.0020 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3656 r_free = 0.3656 target = 0.071431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.058810 restraints weight = 29607.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.060425 restraints weight = 19011.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.061552 restraints weight = 13773.177| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.6798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5845 Z= 0.217 Angle : 0.651 12.657 7935 Z= 0.326 Chirality : 0.046 0.224 877 Planarity : 0.004 0.032 1024 Dihedral : 5.154 29.370 890 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.33), residues: 684 helix: 0.22 (0.88), residues: 40 sheet: 0.01 (0.35), residues: 206 loop : -0.36 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 813 HIS 0.004 0.001 HIS F 199 PHE 0.015 0.001 PHE E 757 TYR 0.013 0.001 TYR F 826 ARG 0.009 0.000 ARG F 851 ********************** 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 78 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 826 TYR cc_start: 0.8336 (m-10) cc_final: 0.8107 (m-80) REVERT: E 845 LYS cc_start: 0.9411 (tmmt) cc_final: 0.9062 (mttt) REVERT: F 38 MET cc_start: 0.7886 (mmt) cc_final: 0.7621 (mmp) REVERT: F 94 VAL cc_start: 0.9487 (t) cc_final: 0.9268 (p) REVERT: F 125 LEU cc_start: 0.8493 (tp) cc_final: 0.8180 (tp) REVERT: F 246 TYR cc_start: 0.8529 (m-80) cc_final: 0.8114 (m-80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1885 time to fit residues: 19.4197 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 : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.5993 > 50: distance: 21 - 84: 14.113 distance: 24 - 81: 10.583 distance: 52 - 58: 4.169 distance: 59 - 60: 15.023 distance: 59 - 62: 14.132 distance: 60 - 61: 14.026 distance: 60 - 67: 16.330 distance: 62 - 63: 11.023 distance: 63 - 64: 4.387 distance: 64 - 65: 4.852 distance: 67 - 68: 9.673 distance: 68 - 69: 15.167 distance: 68 - 71: 23.705 distance: 69 - 70: 18.463 distance: 69 - 81: 17.621 distance: 71 - 72: 10.500 distance: 72 - 73: 7.821 distance: 72 - 74: 8.679 distance: 73 - 75: 6.352 distance: 74 - 76: 3.796 distance: 74 - 77: 3.136 distance: 77 - 79: 5.854 distance: 78 - 80: 3.293 distance: 81 - 82: 14.178 distance: 82 - 83: 21.039 distance: 82 - 85: 22.639 distance: 83 - 84: 20.686 distance: 83 - 90: 10.403 distance: 85 - 86: 17.376 distance: 86 - 87: 5.406 distance: 87 - 88: 6.309 distance: 88 - 89: 3.768 distance: 90 - 91: 3.066 distance: 91 - 92: 18.667 distance: 91 - 94: 6.629 distance: 92 - 93: 18.754 distance: 92 - 97: 24.125 distance: 94 - 95: 10.970 distance: 95 - 96: 5.809 distance: 97 - 98: 11.855 distance: 97 - 103: 22.130 distance: 98 - 99: 20.301 distance: 98 - 101: 12.246 distance: 99 - 100: 19.936 distance: 99 - 104: 39.523 distance: 101 - 102: 19.229 distance: 102 - 103: 8.936 distance: 104 - 105: 9.827 distance: 105 - 106: 18.862 distance: 105 - 108: 29.119 distance: 106 - 107: 17.149 distance: 106 - 110: 40.443 distance: 108 - 109: 27.301 distance: 110 - 111: 28.976 distance: 111 - 112: 25.038 distance: 111 - 114: 28.404 distance: 112 - 113: 31.111 distance: 112 - 118: 26.335 distance: 114 - 115: 15.104 distance: 115 - 116: 18.731 distance: 115 - 117: 17.562 distance: 118 - 124: 10.627 distance: 119 - 120: 24.291 distance: 119 - 122: 9.570 distance: 120 - 121: 28.177 distance: 120 - 125: 27.735 distance: 122 - 123: 7.737 distance: 123 - 124: 19.962 distance: 125 - 126: 17.490 distance: 126 - 127: 39.687 distance: 126 - 129: 18.711 distance: 127 - 128: 29.909 distance: 127 - 133: 45.804 distance: 129 - 130: 28.617 distance: 130 - 131: 19.723 distance: 130 - 132: 18.040 distance: 133 - 134: 25.517 distance: 134 - 135: 25.633 distance: 135 - 136: 8.558 distance: 135 - 137: 16.171