Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 05:44:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn4_0246/04_2023/6hn4_0246.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn4_0246/04_2023/6hn4_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_0246/04_2023/6hn4_0246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn4_0246/04_2023/6hn4_0246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn4_0246/04_2023/6hn4_0246.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hn4_0246/04_2023/6hn4_0246.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-4938/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 chiralities: 6 Time building chain proxies: 4.06, per 1000 atoms: 0.71 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: 2.00 Conformation dependent library (CDL) restraints added in 846.8 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: 0.43 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: 1.74 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: 3292 14.98 - 29.96: 178 29.96 - 44.94: 33 44.94 - 59.92: 7 59.92 - 74.90: 3 Dihedral angle restraints: 3513 sinusoidal: 1465 harmonic: 2048 Sorted by residual: dihedral pdb=" CB CYS E 647 " pdb=" SG CYS E 647 " pdb=" SG CYS E 841 " pdb=" CB CYS E 841 " ideal model delta sinusoidal sigma weight residual 93.00 164.92 -71.92 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" C THR F 771 " pdb=" N THR F 771 " pdb=" CA THR F 771 " pdb=" CB THR F 771 " ideal model delta harmonic sigma weight residual -122.00 -135.47 13.47 0 2.50e+00 1.60e-01 2.90e+01 dihedral pdb=" SG CYS F 304 " pdb=" CB CYS F 308 " pdb=" SG CYS F 308 " pdb=" CA CYS F 308 " ideal model delta sinusoidal sigma weight residual 79.00 4.10 74.90 1 2.00e+01 2.50e-03 1.77e+01 ... (remaining 3510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 632 0.075 - 0.149: 203 0.149 - 0.224: 34 0.224 - 0.299: 7 0.299 - 0.373: 1 Chirality restraints: 877 Sorted by residual: chirality pdb=" CA THR F 771 " pdb=" N THR F 771 " pdb=" C THR F 771 " pdb=" CB THR F 771 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CB VAL F 146 " pdb=" CA VAL F 146 " pdb=" CG1 VAL F 146 " pdb=" CG2 VAL F 146 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA GLU F 773 " pdb=" N GLU F 773 " pdb=" C GLU F 773 " pdb=" CB GLU F 773 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 874 not shown) Planarity restraints: 1030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU F 818 " -0.016 2.00e-02 2.50e+03 3.13e-02 9.78e+00 pdb=" CD GLU F 818 " 0.054 2.00e-02 2.50e+03 pdb=" OE1 GLU F 818 " -0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU F 818 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 612 " -0.015 2.00e-02 2.50e+03 3.11e-02 9.66e+00 pdb=" C ILE E 612 " 0.054 2.00e-02 2.50e+03 pdb=" O ILE E 612 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU E 613 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 612 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.33e+00 pdb=" C ILE F 612 " -0.053 2.00e-02 2.50e+03 pdb=" O ILE F 612 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU F 613 " 0.017 2.00e-02 2.50e+03 ... (remaining 1027 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 327 2.73 - 3.27: 5041 3.27 - 3.81: 9021 3.81 - 4.36: 10732 4.36 - 4.90: 18402 Nonbonded interactions: 43523 Sorted by model distance: nonbonded pdb=" OH TYR E 781 " pdb=" OH TYR F 67 " model vdw 2.187 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: 0.970 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: 5.230 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.490 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.660 ------------------------------------------------------------------------------- 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 : 9.754 69.511 2133 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 1.75 % Allowed : 6.87 % Favored : 91.37 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 0.747 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 outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2161 time to fit residues: 46.3265 Evaluate side-chains 88 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.732 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9873 ------------------------------------------------------------------------------- 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: 7.9990 chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 187 HIS F 209 HIS F 610 GLN F 622 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 5845 Z= 0.323 Angle : 0.806 12.580 7935 Z= 0.398 Chirality : 0.048 0.223 877 Planarity : 0.005 0.037 1024 Dihedral : 5.516 30.588 764 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.16 % 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: -0.89 (0.32), residues: 684 helix: -0.51 (1.03), residues: 28 sheet: -0.88 (0.34), residues: 193 loop : -0.41 (0.30), residues: 463 *********************** 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 106 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.2220 time to fit residues: 29.4992 Evaluate side-chains 72 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.681 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9898 ------------------------------------------------------------------------------- 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: 2.9990 chunk 19 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 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 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 5845 Z= 0.284 Angle : 0.720 10.411 7935 Z= 0.358 Chirality : 0.047 0.152 877 Planarity : 0.004 0.032 1024 Dihedral : 5.232 23.503 764 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 0.00 % 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: -0.44 (0.32), residues: 684 helix: 0.24 (1.11), residues: 28 sheet: -0.37 (0.36), residues: 195 loop : -0.22 (0.30), residues: 461 *********************** 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 86 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1749 time to fit residues: 20.0318 Evaluate side-chains 60 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.687 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9807 ------------------------------------------------------------------------------- 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: 6.9990 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 0.0770 chunk 63 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 5845 Z= 0.215 Angle : 0.659 9.600 7935 Z= 0.327 Chirality : 0.046 0.233 877 Planarity : 0.004 0.030 1024 Dihedral : 5.034 19.781 764 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 0.16 % 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: -0.15 (0.33), residues: 684 helix: 0.43 (1.04), residues: 28 sheet: 0.03 (0.37), residues: 193 loop : -0.13 (0.30), residues: 463 *********************** 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 fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.1622 time to fit residues: 18.5931 Evaluate side-chains 61 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.681 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0220 ------------------------------------------------------------------------------- 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: 8.9990 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 HIS ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 769 GLN ** F 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.5935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.084 5845 Z= 0.568 Angle : 0.909 11.078 7935 Z= 0.459 Chirality : 0.051 0.220 877 Planarity : 0.006 0.054 1024 Dihedral : 5.956 27.953 764 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer Outliers : 0.00 % 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: -0.79 (0.32), residues: 684 helix: 0.06 (0.92), residues: 34 sheet: -0.24 (0.37), residues: 193 loop : -0.68 (0.29), residues: 457 *********************** 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 77 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1708 time to fit residues: 17.9542 Evaluate side-chains 47 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.648 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8738 ------------------------------------------------------------------------------- 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: 5.9990 chunk 67 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7295 moved from start: 0.6011 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= 0.210 Angle : 0.664 9.575 7935 Z= 0.335 Chirality : 0.047 0.229 877 Planarity : 0.004 0.043 1024 Dihedral : 5.291 21.926 764 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer Outliers : 0.00 % 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: -0.41 (0.33), residues: 684 helix: 0.66 (0.91), residues: 34 sheet: -0.17 (0.37), residues: 201 loop : -0.34 (0.31), residues: 449 *********************** 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 75 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1822 time to fit residues: 18.3055 Evaluate side-chains 54 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.714 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9686 ------------------------------------------------------------------------------- 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: 0.3980 chunk 57 optimal weight: 6.9990 chunk 37 optimal weight: 0.1980 chunk 67 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 41 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.6033 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= 0.174 Angle : 0.642 9.659 7935 Z= 0.320 Chirality : 0.047 0.232 877 Planarity : 0.003 0.027 1024 Dihedral : 4.996 18.012 764 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer Outliers : 0.00 % 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: -0.13 (0.34), residues: 684 helix: 1.81 (1.01), residues: 28 sheet: -0.08 (0.36), residues: 211 loop : -0.14 (0.32), residues: 445 *********************** 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 77 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1712 time to fit residues: 17.9480 Evaluate side-chains 56 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.716 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9692 ------------------------------------------------------------------------------- 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: 4.9990 chunk 42 optimal weight: 0.0770 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 635 GLN E 814 GLN F 199 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.6421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 5845 Z= 0.324 Angle : 0.712 9.658 7935 Z= 0.355 Chirality : 0.048 0.240 877 Planarity : 0.004 0.039 1024 Dihedral : 5.221 20.082 764 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer Outliers : 0.16 % 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: -0.27 (0.34), residues: 684 helix: 1.09 (0.98), residues: 34 sheet: -0.18 (0.36), residues: 211 loop : -0.21 (0.32), residues: 439 *********************** 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 72 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.1521 time to fit residues: 15.4477 Evaluate side-chains 46 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9768 ------------------------------------------------------------------------------- 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: 0.7980 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 635 GLN ** F 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.6520 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= 0.204 Angle : 0.641 7.806 7935 Z= 0.322 Chirality : 0.046 0.237 877 Planarity : 0.004 0.028 1024 Dihedral : 5.038 18.881 764 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer Outliers : 0.00 % 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: -0.19 (0.34), residues: 684 helix: 1.10 (0.97), residues: 34 sheet: -0.10 (0.37), residues: 211 loop : -0.17 (0.32), residues: 439 *********************** 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 75 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.671 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1945 time to fit residues: 20.0554 Evaluate side-chains 48 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9639 ------------------------------------------------------------------------------- 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: 0.0060 chunk 55 optimal weight: 0.0170 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.5834 ------------------------------------------------------------------------------- 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: 0.7292 moved from start: 0.6537 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 : 0.630 7.891 7935 Z= 0.316 Chirality : 0.046 0.234 877 Planarity : 0.003 0.027 1024 Dihedral : 4.886 18.891 764 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer Outliers : 0.00 % 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: -0.39 (0.33), residues: 684 helix: -0.45 (0.79), residues: 48 sheet: 0.07 (0.37), residues: 205 loop : -0.34 (0.31), residues: 431 ********************** 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 76 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1757 time to fit residues: 18.1310 Evaluate side-chains 54 residues out of total 638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.726 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9747 ------------------------------------------------------------------------------- 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: 0.9990 chunk 55 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 40 optimal weight: 0.0980 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.072899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.060375 restraints weight = 28996.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.062007 restraints weight = 18717.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.063145 restraints weight = 13495.545| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.6652 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= 0.190 Angle : 0.623 8.007 7935 Z= 0.312 Chirality : 0.046 0.232 877 Planarity : 0.003 0.024 1024 Dihedral : 4.835 18.404 764 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer Outliers : 0.00 % 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: -0.37 (0.33), residues: 684 helix: -0.39 (0.79), residues: 48 sheet: 0.09 (0.37), residues: 210 loop : -0.35 (0.31), residues: 426 =============================================================================== Job complete usr+sys time: 1495.06 seconds wall clock time: 27 minutes 43.75 seconds (1663.75 seconds total)