Starting phenix.real_space_refine on Sun Mar 10 22:42:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn4_0246/03_2024/6hn4_0246.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn4_0246/03_2024/6hn4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn4_0246/03_2024/6hn4_0246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn4_0246/03_2024/6hn4_0246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn4_0246/03_2024/6hn4_0246.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn4_0246/03_2024/6hn4_0246.pdb" } 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 Residue "E TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 844": "NH1" <-> "NH2" Residue "E TYR 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 844": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5702 Number of models: 1 Model: "" Number of chains: 2 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: 4073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4073 Unusual residues: {'NAG': 6} Classifications: {'peptide': 498, 'undetermined': 6} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 466, None: 6} Not linked: pdbres="ASP F 888 " pdbres="NAG F1001 " Not linked: pdbres="NAG F1001 " pdbres="NAG F1002 " Not linked: pdbres="NAG F1002 " pdbres="NAG F1003 " Not linked: pdbres="NAG F1003 " pdbres="NAG F1004 " Not linked: pdbres="NAG F1004 " pdbres="NAG F1005 " Not linked: pdbres="NAG F1005 " pdbres="NAG F1006 " Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 3.83, per 1000 atoms: 0.67 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 - 3.50 Amino acid : False - 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: 2.06 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.85 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: 1.83 Time building geometry restraints manager: 2.22 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: 97.70 - 107.44: 387 107.44 - 117.18: 3893 117.18 - 126.92: 3534 126.92 - 136.66: 119 136.66 - 146.40: 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 2.440 nonbonded pdb=" OG SER F 829 " pdb=" O ARG F 866 " model vdw 2.323 2.440 nonbonded pdb=" OG SER E 829 " pdb=" O ARG E 866 " model vdw 2.339 2.440 nonbonded pdb=" NE2 GLN F 610 " pdb=" OG SER F 752 " model vdw 2.340 2.520 nonbonded pdb=" O SER E 859 " pdb=" OH TYR E 863 " model vdw 2.368 2.440 ... (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 ========== 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: 1.220 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: 0.010 Extract box with map and model: 5.070 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 20.350 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.980 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.533 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: 0.2142 time to fit residues: 45.8055 Evaluate side-chains 96 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 ASN ** F 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 HIS F 610 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5845 Z= 0.223 Angle : 0.741 14.555 7935 Z= 0.367 Chirality : 0.048 0.237 877 Planarity : 0.004 0.038 1024 Dihedral : 5.954 39.326 890 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % 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 (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: -0.89 (0.32), residues: 684 helix: -0.47 (1.02), residues: 28 sheet: -0.93 (0.34), residues: 194 loop : -0.39 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 878 HIS 0.006 0.001 HIS F 264 PHE 0.013 0.001 PHE F 64 TYR 0.013 0.001 TYR F 60 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 117 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.696 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 599 LEU cc_start: 0.9100 (mm) cc_final: 0.8820 (mm) REVERT: E 638 ASP cc_start: 0.6685 (m-30) cc_final: 0.5983 (m-30) REVERT: E 740 PHE cc_start: 0.8960 (p90) cc_final: 0.8633 (p90) REVERT: E 812 MET cc_start: 0.9499 (mtm) cc_final: 0.9104 (mpp) REVERT: E 826 TYR cc_start: 0.8869 (m-80) cc_final: 0.8300 (m-80) REVERT: E 827 GLU cc_start: 0.6516 (tp30) cc_final: 0.6195 (mm-30) REVERT: F 38 MET cc_start: 0.8882 (mtt) cc_final: 0.8277 (mmt) REVERT: F 42 ARG cc_start: 0.9197 (mmm160) cc_final: 0.8944 (mmm160) REVERT: F 125 LEU cc_start: 0.8999 (tp) cc_final: 0.8673 (tp) REVERT: F 131 ILE cc_start: 0.7815 (mt) cc_final: 0.7511 (mm) REVERT: F 154 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7264 (tp30) REVERT: F 246 TYR cc_start: 0.8703 (m-80) cc_final: 0.8458 (m-80) REVERT: F 600 ASP cc_start: 0.8374 (m-30) cc_final: 0.7987 (t0) REVERT: F 616 LYS cc_start: 0.9456 (mptt) cc_final: 0.9249 (mmmt) REVERT: F 641 LEU cc_start: 0.9130 (mp) cc_final: 0.8790 (mt) REVERT: F 757 PHE cc_start: 0.8767 (t80) cc_final: 0.8468 (t80) REVERT: F 787 MET cc_start: 0.8835 (mtt) cc_final: 0.8163 (mtp) REVERT: F 812 MET cc_start: 0.9036 (mtm) cc_final: 0.8624 (mpp) REVERT: F 823 ILE cc_start: 0.7466 (mm) cc_final: 0.6639 (mm) REVERT: F 830 TYR cc_start: 0.8730 (p90) cc_final: 0.8439 (p90) REVERT: F 870 THR cc_start: 0.9317 (m) cc_final: 0.9103 (p) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2421 time to fit residues: 34.8211 Evaluate side-chains 85 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 HIS F 187 HIS ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 622 ASN F 769 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 5845 Z= 0.378 Angle : 0.786 10.073 7935 Z= 0.395 Chirality : 0.050 0.448 877 Planarity : 0.005 0.039 1024 Dihedral : 5.872 29.625 890 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % 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: -0.47 (0.32), residues: 684 helix: -0.18 (0.98), residues: 34 sheet: -0.37 (0.35), residues: 204 loop : -0.22 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 133 HIS 0.009 0.002 HIS E 801 PHE 0.029 0.002 PHE E 757 TYR 0.017 0.002 TYR F 60 ARG 0.004 0.001 ARG E 761 *********************** 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 83 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 600 ASP cc_start: 0.8519 (t0) cc_final: 0.8257 (t0) REVERT: E 740 PHE cc_start: 0.8860 (p90) cc_final: 0.8657 (p90) REVERT: E 800 THR cc_start: 0.8904 (p) cc_final: 0.8622 (p) REVERT: E 826 TYR cc_start: 0.8905 (m-80) cc_final: 0.8533 (m-80) REVERT: F 42 ARG cc_start: 0.9266 (mmm160) cc_final: 0.9017 (mmm160) REVERT: F 125 LEU cc_start: 0.8562 (tp) cc_final: 0.8340 (tp) REVERT: F 600 ASP cc_start: 0.8733 (m-30) cc_final: 0.8252 (t0) REVERT: F 812 MET cc_start: 0.8873 (mtm) cc_final: 0.8642 (mpp) REVERT: F 870 THR cc_start: 0.9295 (m) cc_final: 0.9010 (p) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1982 time to fit residues: 21.2896 Evaluate side-chains 62 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 63 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 765 GLN E 814 GLN E 839 HIS F 123 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.4699 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= 0.188 Angle : 0.650 8.924 7935 Z= 0.326 Chirality : 0.046 0.158 877 Planarity : 0.004 0.033 1024 Dihedral : 5.550 27.536 890 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % 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 (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: -0.22 (0.32), residues: 684 helix: 0.08 (0.93), residues: 34 sheet: 0.03 (0.36), residues: 202 loop : -0.18 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 632 HIS 0.003 0.001 HIS E 756 PHE 0.035 0.002 PHE E 757 TYR 0.011 0.001 TYR F 826 ARG 0.008 0.000 ARG E 831 *********************** 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 90 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.691 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 599 LEU cc_start: 0.9165 (mm) cc_final: 0.8895 (mm) REVERT: E 765 GLN cc_start: 0.7360 (mt0) cc_final: 0.6908 (mm-40) REVERT: E 800 THR cc_start: 0.8938 (p) cc_final: 0.8705 (p) REVERT: E 812 MET cc_start: 0.9126 (mpp) cc_final: 0.8809 (mpp) REVERT: E 817 LYS cc_start: 0.9064 (pttm) cc_final: 0.8486 (tppt) REVERT: E 826 TYR cc_start: 0.8620 (m-80) cc_final: 0.8388 (m-80) REVERT: E 827 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8114 (mm-30) REVERT: F 38 MET cc_start: 0.8574 (mtt) cc_final: 0.7608 (mmm) REVERT: F 125 LEU cc_start: 0.8486 (tp) cc_final: 0.8257 (tp) REVERT: F 600 ASP cc_start: 0.8770 (m-30) cc_final: 0.8221 (t0) REVERT: F 812 MET cc_start: 0.8871 (mtm) cc_final: 0.8533 (mpp) REVERT: F 870 THR cc_start: 0.9257 (m) cc_final: 0.8960 (p) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.1535 time to fit residues: 18.8409 Evaluate side-chains 72 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 0.0970 chunk 39 optimal weight: 0.0670 overall best weight: 1.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5845 Z= 0.303 Angle : 0.681 8.248 7935 Z= 0.347 Chirality : 0.047 0.236 877 Planarity : 0.004 0.031 1024 Dihedral : 5.314 22.764 890 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.21 (0.32), residues: 684 helix: 0.79 (0.94), residues: 34 sheet: 0.16 (0.38), residues: 191 loop : -0.30 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 133 HIS 0.011 0.001 HIS F 199 PHE 0.021 0.002 PHE E 757 TYR 0.018 0.002 TYR E 883 ARG 0.003 0.001 ARG E 761 *********************** 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 80 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 800 THR cc_start: 0.8880 (p) cc_final: 0.8658 (p) REVERT: E 812 MET cc_start: 0.9136 (mpp) cc_final: 0.8868 (mpp) REVERT: E 817 LYS cc_start: 0.9088 (pttm) cc_final: 0.8668 (mmtt) REVERT: E 826 TYR cc_start: 0.8710 (m-80) cc_final: 0.8472 (m-80) REVERT: E 827 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8246 (mm-30) REVERT: E 840 LEU cc_start: 0.7728 (tp) cc_final: 0.7527 (tp) REVERT: F 11 MET cc_start: 0.8373 (mtp) cc_final: 0.8134 (mtp) REVERT: F 125 LEU cc_start: 0.8104 (tp) cc_final: 0.7894 (tp) REVERT: F 600 ASP cc_start: 0.8888 (m-30) cc_final: 0.8425 (t0) REVERT: F 638 ASP cc_start: 0.8854 (m-30) cc_final: 0.8410 (t70) REVERT: F 787 MET cc_start: 0.8678 (mtt) cc_final: 0.7962 (mtt) REVERT: F 812 MET cc_start: 0.8868 (mtm) cc_final: 0.8611 (mpp) REVERT: F 870 THR cc_start: 0.9264 (m) cc_final: 0.8981 (p) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1632 time to fit residues: 17.9845 Evaluate side-chains 62 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 5 optimal weight: 0.0370 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.5589 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= 0.186 Angle : 0.609 7.820 7935 Z= 0.310 Chirality : 0.046 0.219 877 Planarity : 0.003 0.028 1024 Dihedral : 5.061 22.126 890 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % 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 (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: -0.02 (0.33), residues: 684 helix: 1.31 (0.97), residues: 34 sheet: 0.08 (0.36), residues: 207 loop : -0.10 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 632 HIS 0.006 0.001 HIS F 199 PHE 0.014 0.001 PHE E 757 TYR 0.009 0.001 TYR F 60 ARG 0.005 0.000 ARG E 851 *********************** 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 80 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 740 PHE cc_start: 0.8891 (p90) cc_final: 0.8638 (p90) REVERT: E 800 THR cc_start: 0.8909 (p) cc_final: 0.8660 (p) REVERT: E 812 MET cc_start: 0.9062 (mpp) cc_final: 0.8821 (mpp) REVERT: E 827 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8301 (mm-30) REVERT: F 94 VAL cc_start: 0.8926 (t) cc_final: 0.8640 (p) REVERT: F 125 LEU cc_start: 0.8110 (tp) cc_final: 0.7893 (tp) REVERT: F 246 TYR cc_start: 0.8582 (m-80) cc_final: 0.7938 (m-80) REVERT: F 600 ASP cc_start: 0.8925 (m-30) cc_final: 0.8488 (t0) REVERT: F 638 ASP cc_start: 0.8845 (m-30) cc_final: 0.8428 (t70) REVERT: F 812 MET cc_start: 0.8926 (mtm) cc_final: 0.8606 (mpp) REVERT: F 870 THR cc_start: 0.9259 (m) cc_final: 0.8956 (p) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1667 time to fit residues: 18.0215 Evaluate side-chains 62 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 0.0470 chunk 67 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5845 Z= 0.173 Angle : 0.589 7.927 7935 Z= 0.298 Chirality : 0.046 0.226 877 Planarity : 0.003 0.029 1024 Dihedral : 4.766 20.369 890 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % 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: 0.06 (0.33), residues: 684 helix: 1.62 (1.00), residues: 34 sheet: 0.18 (0.37), residues: 203 loop : -0.09 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 632 HIS 0.005 0.001 HIS F 199 PHE 0.011 0.001 PHE F 64 TYR 0.010 0.001 TYR F 830 ARG 0.004 0.000 ARG E 851 *********************** 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 79 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 599 LEU cc_start: 0.9242 (mm) cc_final: 0.8958 (mt) REVERT: E 740 PHE cc_start: 0.8866 (p90) cc_final: 0.8617 (p90) REVERT: E 800 THR cc_start: 0.8890 (p) cc_final: 0.8649 (p) REVERT: E 812 MET cc_start: 0.9071 (mpp) cc_final: 0.8755 (mpp) REVERT: E 827 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8254 (mm-30) REVERT: F 11 MET cc_start: 0.8455 (mtp) cc_final: 0.8228 (mtp) REVERT: F 94 VAL cc_start: 0.8928 (t) cc_final: 0.8642 (p) REVERT: F 125 LEU cc_start: 0.8099 (tp) cc_final: 0.7868 (tp) REVERT: F 246 TYR cc_start: 0.8585 (m-80) cc_final: 0.7952 (m-80) REVERT: F 638 ASP cc_start: 0.8834 (m-30) cc_final: 0.8468 (t70) REVERT: F 787 MET cc_start: 0.8806 (mtt) cc_final: 0.8149 (mtp) REVERT: F 812 MET cc_start: 0.8958 (mtm) cc_final: 0.8599 (mpp) REVERT: F 870 THR cc_start: 0.9265 (m) cc_final: 0.8970 (p) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1701 time to fit residues: 18.0173 Evaluate side-chains 63 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5845 Z= 0.199 Angle : 0.597 7.230 7935 Z= 0.302 Chirality : 0.045 0.221 877 Planarity : 0.004 0.028 1024 Dihedral : 4.718 20.380 890 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.06 (0.34), residues: 684 helix: 1.70 (1.01), residues: 34 sheet: 0.17 (0.37), residues: 203 loop : -0.09 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 813 HIS 0.004 0.001 HIS F 199 PHE 0.011 0.001 PHE F 64 TYR 0.016 0.001 TYR F 826 ARG 0.003 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 80 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 599 LEU cc_start: 0.9190 (mm) cc_final: 0.8958 (mt) REVERT: E 740 PHE cc_start: 0.8910 (p90) cc_final: 0.8673 (p90) REVERT: E 845 LYS cc_start: 0.9449 (tmmt) cc_final: 0.8972 (mtpt) REVERT: F 11 MET cc_start: 0.8562 (mtp) cc_final: 0.8326 (mtp) REVERT: F 38 MET cc_start: 0.8424 (mtt) cc_final: 0.7955 (mmt) REVERT: F 94 VAL cc_start: 0.8914 (t) cc_final: 0.8629 (p) REVERT: F 125 LEU cc_start: 0.8106 (tp) cc_final: 0.7885 (tp) REVERT: F 246 TYR cc_start: 0.8586 (m-80) cc_final: 0.7977 (m-80) REVERT: F 600 ASP cc_start: 0.9179 (m-30) cc_final: 0.8747 (p0) REVERT: F 638 ASP cc_start: 0.8961 (m-30) cc_final: 0.8479 (t70) REVERT: F 787 MET cc_start: 0.8805 (mtt) cc_final: 0.8151 (mtp) REVERT: F 812 MET cc_start: 0.9015 (mtm) cc_final: 0.8620 (mpp) REVERT: F 826 TYR cc_start: 0.9227 (m-80) cc_final: 0.8773 (m-10) REVERT: F 838 LEU cc_start: 0.8571 (mp) cc_final: 0.8370 (tp) REVERT: F 870 THR cc_start: 0.9209 (m) cc_final: 0.8892 (p) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1717 time to fit residues: 18.5226 Evaluate side-chains 63 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 56 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.6047 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= 0.180 Angle : 0.596 7.376 7935 Z= 0.301 Chirality : 0.046 0.226 877 Planarity : 0.003 0.030 1024 Dihedral : 4.661 19.746 890 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % 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: 0.05 (0.34), residues: 684 helix: 1.70 (0.99), residues: 34 sheet: 0.21 (0.37), residues: 203 loop : -0.12 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 813 HIS 0.004 0.001 HIS F 199 PHE 0.022 0.001 PHE E 884 TYR 0.012 0.001 TYR F 826 ARG 0.003 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 79 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 599 LEU cc_start: 0.9203 (mm) cc_final: 0.8955 (mt) REVERT: E 740 PHE cc_start: 0.8955 (p90) cc_final: 0.8722 (p90) REVERT: E 845 LYS cc_start: 0.9451 (tmmt) cc_final: 0.8976 (mtpt) REVERT: E 884 PHE cc_start: 0.8343 (m-10) cc_final: 0.8131 (m-80) REVERT: F 11 MET cc_start: 0.8543 (mtp) cc_final: 0.8317 (mtp) REVERT: F 94 VAL cc_start: 0.8927 (t) cc_final: 0.8644 (p) REVERT: F 125 LEU cc_start: 0.8085 (tp) cc_final: 0.7857 (tp) REVERT: F 246 TYR cc_start: 0.8584 (m-80) cc_final: 0.8020 (m-80) REVERT: F 600 ASP cc_start: 0.9190 (m-30) cc_final: 0.8736 (p0) REVERT: F 638 ASP cc_start: 0.8935 (m-30) cc_final: 0.8466 (t70) REVERT: F 787 MET cc_start: 0.8854 (mtt) cc_final: 0.8242 (mtp) REVERT: F 812 MET cc_start: 0.9048 (mtm) cc_final: 0.8639 (mpp) REVERT: F 826 TYR cc_start: 0.9201 (m-80) cc_final: 0.8784 (m-10) REVERT: F 838 LEU cc_start: 0.8570 (mp) cc_final: 0.8364 (tp) REVERT: F 870 THR cc_start: 0.9185 (m) cc_final: 0.8873 (p) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1691 time to fit residues: 18.0205 Evaluate side-chains 60 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 5 optimal weight: 0.0040 chunk 42 optimal weight: 0.4980 chunk 34 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.6170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 5845 Z= 0.164 Angle : 0.584 7.063 7935 Z= 0.296 Chirality : 0.045 0.223 877 Planarity : 0.003 0.030 1024 Dihedral : 4.538 19.238 890 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.04 (0.33), residues: 684 helix: 0.81 (0.89), residues: 40 sheet: 0.36 (0.37), residues: 203 loop : -0.16 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 813 HIS 0.004 0.001 HIS F 199 PHE 0.021 0.001 PHE E 884 TYR 0.012 0.001 TYR F 826 ARG 0.004 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 79 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 599 LEU cc_start: 0.9211 (mm) cc_final: 0.8980 (mt) REVERT: E 740 PHE cc_start: 0.8949 (p90) cc_final: 0.8724 (p90) REVERT: E 845 LYS cc_start: 0.9462 (tmmt) cc_final: 0.8988 (mtpt) REVERT: F 11 MET cc_start: 0.8406 (mtp) cc_final: 0.8169 (mtp) REVERT: F 94 VAL cc_start: 0.8924 (t) cc_final: 0.8648 (p) REVERT: F 125 LEU cc_start: 0.8200 (tp) cc_final: 0.7988 (tp) REVERT: F 246 TYR cc_start: 0.8576 (m-80) cc_final: 0.8020 (m-80) REVERT: F 600 ASP cc_start: 0.9193 (m-30) cc_final: 0.8744 (p0) REVERT: F 638 ASP cc_start: 0.8970 (m-30) cc_final: 0.8505 (t70) REVERT: F 787 MET cc_start: 0.8885 (mtt) cc_final: 0.8268 (mtp) REVERT: F 812 MET cc_start: 0.9104 (mtm) cc_final: 0.8683 (mpp) REVERT: F 826 TYR cc_start: 0.9129 (m-80) cc_final: 0.8634 (m-10) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1705 time to fit residues: 18.1279 Evaluate side-chains 56 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 801 HIS F 199 HIS ** F 218 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 = 0.3676 r_free = 0.3676 target = 0.072370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.059492 restraints weight = 29350.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.061065 restraints weight = 19053.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.062193 restraints weight = 13924.528| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.6406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5845 Z= 0.254 Angle : 0.629 7.083 7935 Z= 0.319 Chirality : 0.046 0.228 877 Planarity : 0.004 0.030 1024 Dihedral : 4.864 20.243 890 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % 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: 0.11 (0.34), residues: 684 helix: 1.60 (0.97), residues: 34 sheet: 0.25 (0.36), residues: 208 loop : -0.07 (0.32), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 878 HIS 0.004 0.001 HIS F 199 PHE 0.017 0.002 PHE E 884 TYR 0.016 0.002 TYR E 883 ARG 0.004 0.001 ARG F 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1537.90 seconds wall clock time: 28 minutes 29.32 seconds (1709.32 seconds total)