Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 23:50:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzo_0559/04_2023/6nzo_0559.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzo_0559/04_2023/6nzo_0559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzo_0559/04_2023/6nzo_0559.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzo_0559/04_2023/6nzo_0559.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzo_0559/04_2023/6nzo_0559.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzo_0559/04_2023/6nzo_0559.pdb" } resolution = 3.8 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= 0.003 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 290 5.49 5 S 32 5.16 5 C 7707 2.51 5 N 2563 2.21 5 O 3143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 97": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H GLU 90": "OE1" <-> "OE2" 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: 13738 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 629 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 797 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 834 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 792 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 752 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2988 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "S" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1819 Unusual residues: {' ZN': 3} Classifications: {'peptide': 233, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 223, None: 3} Not linked: pdbres="THR S 325 " pdbres=" ZN S1001 " Not linked: pdbres=" ZN S1001 " pdbres=" ZN S1002 " Not linked: pdbres=" ZN S1002 " pdbres=" ZN S1003 " Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12284 SG CYS S 143 60.709 80.388 47.265 1.00109.22 S ATOM 12396 SG CYS S 158 59.164 84.192 47.848 1.00101.19 S ATOM 12429 SG CYS S 163 61.766 82.563 50.683 1.00113.64 S ATOM 12466 SG CYS S 169 61.843 82.802 46.265 1.00112.25 S ATOM 12173 SG CYS S 129 58.781 80.486 51.064 1.00112.66 S ATOM 12187 SG CYS S 131 58.804 77.494 49.481 1.00118.61 S ATOM 12284 SG CYS S 143 60.709 80.388 47.265 1.00109.22 S ATOM 12325 SG CYS S 149 58.199 78.606 47.178 1.00 92.28 S ATOM 13234 SG CYS S 261 37.901 89.429 19.020 1.00124.70 S ATOM 13613 SG CYS S 308 40.146 91.851 16.557 1.00133.16 S ATOM 13631 SG CYS S 310 40.500 89.796 15.425 1.00135.88 S ATOM 13665 SG CYS S 315 37.577 90.841 15.137 1.00131.95 S Time building chain proxies: 7.51, per 1000 atoms: 0.55 Number of scatterers: 13738 At special positions: 0 Unit cell: (83.2, 146.64, 131.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 32 16.00 P 290 15.00 O 3143 8.00 N 2563 7.00 C 7707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 7.59 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN S1001 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 169 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 143 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 158 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 163 " pdb=" ZN S1002 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 129 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 149 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 143 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 131 " pdb=" ZN S1003 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 308 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 315 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 310 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 261 " Number of angles added : 18 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 14 sheets defined 58.8% alpha, 5.8% beta 143 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 5.79 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.962A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.552A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.718A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 17 through 21' Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.561A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.633A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.003A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.501A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.926A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.392A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.521A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.546A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 151 through 155 removed outlier: 3.601A pdb=" N LYS S 155 " --> pdb=" O ARG S 152 " (cutoff:3.500A) Processing helix chain 'S' and resid 215 through 230 Processing helix chain 'S' and resid 252 through 256 removed outlier: 3.607A pdb=" N ARG S 255 " --> pdb=" O ASN S 252 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE S 256 " --> pdb=" O LEU S 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 252 through 256' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.828A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.107A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.726A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AA8, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.271A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.082A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'S' and resid 182 through 187 Processing sheet with id=AB4, first strand: chain 'S' and resid 205 through 208 removed outlier: 6.715A pdb=" N PHE S 205 " --> pdb=" O ALA S 282 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA S 282 " --> pdb=" O PHE S 205 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 212 through 214 443 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 5.65 Time building geometry restraints manager: 7.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2233 1.33 - 1.45: 4991 1.45 - 1.57: 6723 1.57 - 1.69: 578 1.69 - 1.81: 46 Bond restraints: 14571 Sorted by residual: bond pdb=" C ASP S 134 " pdb=" N TRP S 135 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.23e-02 6.61e+03 2.32e+01 bond pdb=" C ILE G 79 " pdb=" N PRO G 80 " ideal model delta sigma weight residual 1.334 1.392 -0.058 1.51e-02 4.39e+03 1.45e+01 bond pdb=" C3' DC I 143 " pdb=" O3' DC I 143 " ideal model delta sigma weight residual 1.422 1.500 -0.078 3.00e-02 1.11e+03 6.72e+00 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.495 -0.073 3.00e-02 1.11e+03 5.95e+00 bond pdb=" C ILE E 51 " pdb=" N ARG E 52 " ideal model delta sigma weight residual 1.335 1.366 -0.032 1.36e-02 5.41e+03 5.42e+00 ... (remaining 14566 not shown) Histogram of bond angle deviations from ideal: 98.04 - 105.48: 1460 105.48 - 112.92: 7993 112.92 - 120.36: 6086 120.36 - 127.81: 4928 127.81 - 135.25: 442 Bond angle restraints: 20909 Sorted by residual: angle pdb=" N PRO S 88 " pdb=" CA PRO S 88 " pdb=" CB PRO S 88 " ideal model delta sigma weight residual 103.00 110.43 -7.43 1.10e+00 8.26e-01 4.56e+01 angle pdb=" N PRO S 89 " pdb=" CA PRO S 89 " pdb=" CB PRO S 89 " ideal model delta sigma weight residual 103.38 110.40 -7.02 1.05e+00 9.07e-01 4.47e+01 angle pdb=" N PRO S 84 " pdb=" CA PRO S 84 " pdb=" CB PRO S 84 " ideal model delta sigma weight residual 103.00 110.24 -7.24 1.10e+00 8.26e-01 4.33e+01 angle pdb=" C SER S 122 " pdb=" N ASP S 123 " pdb=" CA ASP S 123 " ideal model delta sigma weight residual 122.61 129.82 -7.21 1.56e+00 4.11e-01 2.14e+01 angle pdb=" N VAL S 159 " pdb=" CA VAL S 159 " pdb=" C VAL S 159 " ideal model delta sigma weight residual 110.05 105.60 4.45 1.09e+00 8.42e-01 1.67e+01 ... (remaining 20904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.58: 6265 34.58 - 69.17: 1472 69.17 - 103.75: 15 103.75 - 138.33: 0 138.33 - 172.91: 4 Dihedral angle restraints: 7756 sinusoidal: 4909 harmonic: 2847 Sorted by residual: dihedral pdb=" CA GLN S 172 " pdb=" C GLN S 172 " pdb=" N ARG S 173 " pdb=" CA ARG S 173 " ideal model delta harmonic sigma weight residual 180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA GLU S 133 " pdb=" C GLU S 133 " pdb=" N ASP S 134 " pdb=" CA ASP S 134 " ideal model delta harmonic sigma weight residual 180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 47.09 172.91 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1700 0.056 - 0.112: 531 0.112 - 0.168: 91 0.168 - 0.224: 23 0.224 - 0.280: 6 Chirality restraints: 2351 Sorted by residual: chirality pdb=" CB ILE H 51 " pdb=" CA ILE H 51 " pdb=" CG1 ILE H 51 " pdb=" CG2 ILE H 51 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE G 111 " pdb=" CA ILE G 111 " pdb=" CG1 ILE G 111 " pdb=" CG2 ILE G 111 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA GLU S 216 " pdb=" N GLU S 216 " pdb=" C GLU S 216 " pdb=" CB GLU S 216 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 2348 not shown) Planarity restraints: 1659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 102 " -0.038 2.00e-02 2.50e+03 1.77e-02 9.39e+00 pdb=" N9 DG I 102 " 0.032 2.00e-02 2.50e+03 pdb=" C8 DG I 102 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 102 " 0.023 2.00e-02 2.50e+03 pdb=" C5 DG I 102 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 102 " -0.021 2.00e-02 2.50e+03 pdb=" O6 DG I 102 " -0.012 2.00e-02 2.50e+03 pdb=" N1 DG I 102 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DG I 102 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 102 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DG I 102 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG I 102 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " -0.040 2.00e-02 2.50e+03 1.78e-02 8.71e+00 pdb=" N9 DA I 20 " 0.039 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.007 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " -0.012 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 106 " 0.037 2.00e-02 2.50e+03 1.61e-02 7.82e+00 pdb=" N9 DG J 106 " -0.038 2.00e-02 2.50e+03 pdb=" C8 DG J 106 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG J 106 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG J 106 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DG J 106 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG J 106 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DG J 106 " 0.007 2.00e-02 2.50e+03 pdb=" C2 DG J 106 " -0.010 2.00e-02 2.50e+03 pdb=" N2 DG J 106 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG J 106 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG J 106 " -0.004 2.00e-02 2.50e+03 ... (remaining 1656 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3615 2.83 - 3.35: 11979 3.35 - 3.87: 27098 3.87 - 4.38: 30302 4.38 - 4.90: 43766 Nonbonded interactions: 116760 Sorted by model distance: nonbonded pdb=" O CYS S 129 " pdb=" ND2 ASN S 164 " model vdw 2.313 2.520 nonbonded pdb=" O SER D 120 " pdb=" OG SER D 120 " model vdw 2.322 2.440 nonbonded pdb=" O SER S 260 " pdb=" ND2 ASN S 295 " model vdw 2.333 2.520 nonbonded pdb=" CB THR H 29 " pdb=" OP1 DT I 104 " model vdw 2.333 3.470 nonbonded pdb=" O LYS S 190 " pdb=" ND2 ASN S 258 " model vdw 2.352 2.520 ... (remaining 116755 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = (chain 'B' and resid 24 through 100) selection = (chain 'F' and resid 24 through 100) } ncs_group { reference = (chain 'C' and resid 16 through 118) selection = (chain 'G' and (resid 16 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = (chain 'D' and resid 26 through 120) selection = chain 'H' } 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=0.89 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 4.220 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 46.650 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 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 0.078 14571 Z= 0.401 Angle : 0.926 10.246 20909 Z= 0.563 Chirality : 0.056 0.280 2351 Planarity : 0.007 0.056 1659 Dihedral : 27.119 172.914 5924 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.79 % Favored : 95.11 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.08 (0.24), residues: 961 helix: 0.15 (0.19), residues: 551 sheet: -2.07 (0.76), residues: 45 loop : -1.82 (0.28), residues: 365 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.3822 time to fit residues: 128.2378 Evaluate side-chains 160 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 0.0770 chunk 49 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 106 HIS E 68 GLN E 85 GLN F 75 HIS G 24 GLN G 38 ASN ** S 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 215 ASN S 242 ASN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 14571 Z= 0.178 Angle : 0.577 7.246 20909 Z= 0.343 Chirality : 0.035 0.207 2351 Planarity : 0.005 0.060 1659 Dihedral : 30.440 172.555 4008 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.27), residues: 961 helix: 1.97 (0.21), residues: 558 sheet: -1.69 (0.81), residues: 45 loop : -1.41 (0.31), residues: 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 212 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 223 average time/residue: 0.2905 time to fit residues: 90.2597 Evaluate side-chains 191 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 178 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1318 time to fit residues: 4.4491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 85 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 242 ASN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.065 14571 Z= 0.473 Angle : 0.781 7.656 20909 Z= 0.446 Chirality : 0.045 0.195 2351 Planarity : 0.006 0.061 1659 Dihedral : 30.997 178.280 4008 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer Outliers : 4.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.26), residues: 961 helix: 1.25 (0.21), residues: 552 sheet: -1.65 (0.84), residues: 45 loop : -1.42 (0.31), residues: 364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 197 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 25 residues processed: 214 average time/residue: 0.2892 time to fit residues: 86.6401 Evaluate side-chains 197 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 172 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1218 time to fit residues: 7.1125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN G 38 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 242 ASN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 14571 Z= 0.238 Angle : 0.632 10.163 20909 Z= 0.367 Chirality : 0.037 0.164 2351 Planarity : 0.005 0.057 1659 Dihedral : 30.800 174.310 4008 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.27), residues: 961 helix: 1.71 (0.22), residues: 553 sheet: -1.63 (0.82), residues: 45 loop : -1.33 (0.32), residues: 363 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 198 average time/residue: 0.2752 time to fit residues: 77.4395 Evaluate side-chains 184 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1488 time to fit residues: 4.9225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 112 GLN E 85 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 242 ASN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 14571 Z= 0.182 Angle : 0.585 9.471 20909 Z= 0.342 Chirality : 0.035 0.144 2351 Planarity : 0.005 0.056 1659 Dihedral : 30.520 173.121 4008 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.02 (0.28), residues: 961 helix: 1.99 (0.22), residues: 556 sheet: -1.64 (0.81), residues: 45 loop : -1.16 (0.32), residues: 360 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 191 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 198 average time/residue: 0.2720 time to fit residues: 77.0253 Evaluate side-chains 178 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 172 time to evaluate : 1.162 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1721 time to fit residues: 3.1433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.4980 chunk 23 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 118 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 9 optimal weight: 0.0870 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 overall best weight: 1.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 233 HIS S 242 ASN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 14571 Z= 0.219 Angle : 0.597 6.724 20909 Z= 0.348 Chirality : 0.036 0.186 2351 Planarity : 0.004 0.050 1659 Dihedral : 30.557 174.023 4008 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.28), residues: 961 helix: 1.95 (0.22), residues: 556 sheet: -1.56 (0.85), residues: 40 loop : -1.14 (0.32), residues: 365 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 1.153 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 186 average time/residue: 0.2772 time to fit residues: 73.3254 Evaluate side-chains 176 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 166 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1300 time to fit residues: 3.6301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 50.0000 chunk 65 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 14571 Z= 0.280 Angle : 0.650 10.136 20909 Z= 0.372 Chirality : 0.038 0.199 2351 Planarity : 0.005 0.050 1659 Dihedral : 30.767 179.610 4008 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.67 (0.27), residues: 961 helix: 1.59 (0.21), residues: 559 sheet: -1.73 (0.84), residues: 40 loop : -1.14 (0.32), residues: 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 176 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 183 average time/residue: 0.2863 time to fit residues: 73.9655 Evaluate side-chains 174 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 165 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1288 time to fit residues: 3.5049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 58 optimal weight: 0.0570 chunk 10 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 172 GLN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 14571 Z= 0.181 Angle : 0.593 9.300 20909 Z= 0.341 Chirality : 0.036 0.183 2351 Planarity : 0.004 0.049 1659 Dihedral : 30.587 174.597 4008 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.02 (0.28), residues: 961 helix: 1.91 (0.22), residues: 554 sheet: -1.70 (0.80), residues: 40 loop : -1.00 (0.33), residues: 367 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 187 average time/residue: 0.2773 time to fit residues: 74.0817 Evaluate side-chains 179 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 172 time to evaluate : 1.243 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1363 time to fit residues: 3.2209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 50.0000 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 172 GLN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 14571 Z= 0.312 Angle : 0.667 8.473 20909 Z= 0.380 Chirality : 0.038 0.174 2351 Planarity : 0.005 0.048 1659 Dihedral : 30.785 179.058 4008 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.69 (0.27), residues: 961 helix: 1.59 (0.21), residues: 558 sheet: -1.82 (0.81), residues: 40 loop : -1.06 (0.33), residues: 363 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 177 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 180 average time/residue: 0.2792 time to fit residues: 71.0771 Evaluate side-chains 166 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 161 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1345 time to fit residues: 2.7443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 121 optimal weight: 0.0070 chunk 111 optimal weight: 0.0870 chunk 96 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 14571 Z= 0.192 Angle : 0.618 9.717 20909 Z= 0.352 Chirality : 0.036 0.177 2351 Planarity : 0.004 0.050 1659 Dihedral : 30.650 176.119 4008 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.97 (0.27), residues: 961 helix: 1.83 (0.21), residues: 554 sheet: -1.77 (0.79), residues: 40 loop : -0.94 (0.33), residues: 367 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 179 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 182 average time/residue: 0.2758 time to fit residues: 71.6542 Evaluate side-chains 173 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 171 time to evaluate : 1.381 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1616 time to fit residues: 1.9002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.132985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.104414 restraints weight = 30219.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.106688 restraints weight = 16679.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.108162 restraints weight = 11572.198| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3751 r_free = 0.3751 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3751 r_free = 0.3751 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 14571 Z= 0.217 Angle : 0.620 9.395 20909 Z= 0.354 Chirality : 0.036 0.173 2351 Planarity : 0.004 0.050 1659 Dihedral : 30.651 177.632 4008 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.96 (0.27), residues: 961 helix: 1.83 (0.22), residues: 554 sheet: -1.75 (0.80), residues: 40 loop : -0.95 (0.32), residues: 367 =============================================================================== Job complete usr+sys time: 2340.43 seconds wall clock time: 43 minutes 21.84 seconds (2601.84 seconds total)