Starting phenix.real_space_refine on Fri Nov 17 05:16:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca7_16520/11_2023/8ca7_16520_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca7_16520/11_2023/8ca7_16520.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca7_16520/11_2023/8ca7_16520_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca7_16520/11_2023/8ca7_16520_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca7_16520/11_2023/8ca7_16520_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca7_16520/11_2023/8ca7_16520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca7_16520/11_2023/8ca7_16520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca7_16520/11_2023/8ca7_16520_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca7_16520/11_2023/8ca7_16520_updated.pdb" } resolution = 2.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 14 8.98 5 P 502 5.49 5 Mg 26 5.21 5 S 18 5.16 5 C 9045 2.51 5 N 3258 2.21 5 O 5230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 40": "OE1" <-> "OE2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "I GLU 36": "OE1" <-> "OE2" Residue "I ARG 41": "NH1" <-> "NH2" Residue "I GLU 53": "OE1" <-> "OE2" Residue "I GLU 59": "OE1" <-> "OE2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "I GLU 92": "OE1" <-> "OE2" Residue "I ARG 99": "NH1" <-> "NH2" Residue "I ARG 106": "NH1" <-> "NH2" Residue "I ARG 109": "NH1" <-> "NH2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "I ARG 113": "NH1" <-> "NH2" Residue "I ARG 123": "NH1" <-> "NH2" Residue "J GLU 24": "OE1" <-> "OE2" Residue "J GLU 27": "OE1" <-> "OE2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M GLU 50": "OE1" <-> "OE2" Residue "M GLU 59": "OE1" <-> "OE2" Residue "M GLU 66": "OE1" <-> "OE2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "M TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 87": "NH1" <-> "NH2" Residue "N GLU 10": "OE1" <-> "OE2" Residue "N GLU 26": "OE1" <-> "OE2" Residue "N GLU 39": "OE1" <-> "OE2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N GLU 92": "OE1" <-> "OE2" Residue "S GLU 20": "OE1" <-> "OE2" Residue "S GLU 24": "OE1" <-> "OE2" Residue "S ARG 36": "NH1" <-> "NH2" Residue "S ASP 64": "OD1" <-> "OD2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S GLU 73": "OE1" <-> "OE2" Residue "S ARG 81": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 18093 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 10741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 10741 Classifications: {'RNA': 502} Modifications used: {'rna2p_pur': 44, 'rna2p_pyr': 35, 'rna3p': 4, 'rna3p_pur': 228, 'rna3p_pyr': 191} Link IDs: {'rna2p': 79, 'rna3p': 422} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "E" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain breaks: 1 Chain: "G" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 793 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain breaks: 2 Chain: "I" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1001 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "J" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain breaks: 1 Chain: "M" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 876 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 668 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 102 Unusual residues: {' K': 14, ' MG': 25, 'SCM': 1, 'U3B': 1} Classifications: {'undetermined': 41} Link IDs: {None: 40} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 449 Classifications: {'water': 449} Link IDs: {None: 448} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "M" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "N" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "S" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 9.12, per 1000 atoms: 0.50 Number of scatterers: 18093 At special positions: 0 Unit cell: (117.348, 128.016, 125.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 14 19.00 S 18 16.00 P 502 15.00 Mg 26 11.99 O 5230 8.00 N 3258 7.00 C 9045 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: 10.80 Conformation dependent library (CDL) restraints added in 1.2 seconds 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1570 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 8 sheets defined 42.3% alpha, 15.9% beta 153 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 11.00 Creating SS restraints... Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.824A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 11' Processing helix chain 'C' and resid 26 through 46 removed outlier: 4.370A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 79 through 95 removed outlier: 6.237A pdb=" N ASP C 83 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 84 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS C 86 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS C 89 " --> pdb=" O LYS C 86 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 91 " --> pdb=" O ARG C 88 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C 95 " --> pdb=" O ALA C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 113 through 126 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'E' and resid 56 through 64 Processing helix chain 'G' and resid 21 through 30 Processing helix chain 'G' and resid 36 through 52 Processing helix chain 'G' and resid 58 through 69 removed outlier: 3.536A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 110 Processing helix chain 'G' and resid 116 through 125 Processing helix chain 'I' and resid 35 through 38 No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 42 through 55 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 72 through 90 removed outlier: 3.502A pdb=" N GLU I 89 " --> pdb=" O ARG I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 100 Processing helix chain 'J' and resid 15 through 32 removed outlier: 3.503A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 21 removed outlier: 4.088A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 45 through 47 No H-bonds generated for 'chain 'M' and resid 45 through 47' Processing helix chain 'M' and resid 50 through 62 removed outlier: 3.564A pdb=" N ALA M 61 " --> pdb=" O ARG M 57 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 83 Processing helix chain 'M' and resid 86 through 93 Processing helix chain 'M' and resid 107 through 110 No H-bonds generated for 'chain 'M' and resid 107 through 110' Processing helix chain 'N' and resid 4 through 19 Processing helix chain 'N' and resid 21 through 32 Processing helix chain 'N' and resid 38 through 50 removed outlier: 3.584A pdb=" N GLN N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 55 No H-bonds generated for 'chain 'N' and resid 53 through 55' Processing helix chain 'N' and resid 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing helix chain 'N' and resid 81 through 89 Processing helix chain 'S' and resid 13 through 25 Processing helix chain 'S' and resid 42 through 44 No H-bonds generated for 'chain 'S' and resid 42 through 44' Processing helix chain 'S' and resid 71 through 74 Processing sheet with id= A, first strand: chain 'C' and resid 99 through 105 removed outlier: 6.527A pdb=" N ILE C 64 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ASN C 102 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ALA C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE C 68 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 164 through 171 Processing sheet with id= C, first strand: chain 'E' and resid 20 through 25 removed outlier: 3.985A pdb=" N ALA E 35 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY E 51 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'I' and resid 6 through 12 Processing sheet with id= E, first strand: chain 'J' and resid 96 through 101 removed outlier: 3.515A pdb=" N ARG J 7 " --> pdb=" O SER J 101 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP J 75 " --> pdb=" O ARG J 37 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'J' and resid 40 through 42 removed outlier: 4.551A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 45 through 52 Processing sheet with id= H, first strand: chain 'S' and resid 31 through 33 298 hydrogen bonds defined for protein. 831 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 382 hydrogen bonds 608 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 13.82 Time building geometry restraints manager: 11.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2700 1.34 - 1.46: 8578 1.46 - 1.59: 6572 1.59 - 1.71: 997 1.71 - 1.83: 34 Bond restraints: 18881 Sorted by residual: bond pdb=" C6 SCM A1603 " pdb=" O1 SCM A1603 " ideal model delta sigma weight residual 0.917 1.416 -0.499 2.00e-02 2.50e+03 6.22e+02 bond pdb=" C3 SCM A1603 " pdb=" C4 SCM A1603 " ideal model delta sigma weight residual 1.054 1.509 -0.455 2.00e-02 2.50e+03 5.18e+02 bond pdb=" C7 SCM A1603 " pdb=" O1B SCM A1603 " ideal model delta sigma weight residual 1.166 1.429 -0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C6 SCM A1603 " pdb=" O2B SCM A1603 " ideal model delta sigma weight residual 1.165 1.417 -0.252 2.00e-02 2.50e+03 1.59e+02 bond pdb=" C20 U3B A1602 " pdb=" C21 U3B A1602 " ideal model delta sigma weight residual 1.605 1.390 0.215 2.00e-02 2.50e+03 1.15e+02 ... (remaining 18876 not shown) Histogram of bond angle deviations from ideal: 81.86 - 92.53: 2 92.53 - 103.20: 1498 103.20 - 113.87: 12714 113.87 - 124.54: 11518 124.54 - 135.21: 2207 Bond angle restraints: 27939 Sorted by residual: angle pdb=" O3' U A 981 " pdb=" P U A 982 " pdb=" OP2 U A 982 " ideal model delta sigma weight residual 108.00 81.86 26.14 3.00e+00 1.11e-01 7.59e+01 angle pdb=" O3' C A1369 " pdb=" P G A1370 " pdb=" O5' G A1370 " ideal model delta sigma weight residual 104.00 92.15 11.85 1.50e+00 4.44e-01 6.24e+01 angle pdb=" O3' G A1347 " pdb=" P U A1348 " pdb=" O5' U A1348 " ideal model delta sigma weight residual 104.00 92.56 11.44 1.50e+00 4.44e-01 5.82e+01 angle pdb=" O3' U A 981 " pdb=" P U A 982 " pdb=" OP1 U A 982 " ideal model delta sigma weight residual 108.00 129.92 -21.92 3.00e+00 1.11e-01 5.34e+01 angle pdb=" C1' 2MG A1207 " pdb=" N9 2MG A1207 " pdb=" C8 2MG A1207 " ideal model delta sigma weight residual 110.07 129.03 -18.96 3.00e+00 1.11e-01 3.99e+01 ... (remaining 27934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.67: 9868 33.67 - 67.35: 364 67.35 - 101.02: 32 101.02 - 134.69: 0 134.69 - 168.37: 5 Dihedral angle restraints: 10269 sinusoidal: 7847 harmonic: 2422 Sorted by residual: dihedral pdb=" O4' C A1158 " pdb=" C1' C A1158 " pdb=" N1 C A1158 " pdb=" C2 C A1158 " ideal model delta sinusoidal sigma weight residual 200.00 61.99 138.01 1 1.50e+01 4.44e-03 7.44e+01 dihedral pdb=" O4' U A 960 " pdb=" C1' U A 960 " pdb=" N1 U A 960 " pdb=" C2 U A 960 " ideal model delta sinusoidal sigma weight residual 232.00 67.20 164.80 1 1.70e+01 3.46e-03 6.53e+01 dihedral pdb=" C5' A A1319 " pdb=" C4' A A1319 " pdb=" C3' A A1319 " pdb=" O3' A A1319 " ideal model delta sinusoidal sigma weight residual 147.00 105.50 41.50 1 8.00e+00 1.56e-02 3.77e+01 ... (remaining 10266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.983: 3525 0.983 - 1.965: 0 1.965 - 2.948: 0 2.948 - 3.930: 1 3.930 - 4.913: 1 Chirality restraints: 3527 Sorted by residual: chirality pdb=" C5 SCM A1603 " pdb=" C4 SCM A1603 " pdb=" C6 SCM A1603 " pdb=" O1B SCM A1603 " both_signs ideal model delta sigma weight residual False 2.40 -2.52 4.91 2.00e-01 2.50e+01 6.03e+02 chirality pdb=" C6 SCM A1603 " pdb=" C5 SCM A1603 " pdb=" O1 SCM A1603 " pdb=" O2B SCM A1603 " both_signs ideal model delta sigma weight residual False 1.09 -2.31 3.40 2.00e-01 2.50e+01 2.89e+02 chirality pdb=" P A A 919 " pdb=" OP1 A A 919 " pdb=" OP2 A A 919 " pdb=" O5' A A 919 " both_signs ideal model delta sigma weight residual True 2.41 -3.00 -0.59 2.00e-01 2.50e+01 8.72e+00 ... (remaining 3524 not shown) Planarity restraints: 1681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " 0.063 2.00e-02 2.50e+03 5.91e-01 7.86e+03 pdb=" C4' 2MG A1207 " 0.423 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " 0.642 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " -0.628 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " -0.610 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " -0.156 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " 0.950 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " 0.217 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " -0.900 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A 966 " 0.039 2.00e-02 2.50e+03 5.68e-01 7.25e+03 pdb=" C4' 2MG A 966 " 0.431 2.00e-02 2.50e+03 pdb=" O4' 2MG A 966 " 0.673 2.00e-02 2.50e+03 pdb=" C3' 2MG A 966 " -0.612 2.00e-02 2.50e+03 pdb=" O3' 2MG A 966 " -0.542 2.00e-02 2.50e+03 pdb=" C2' 2MG A 966 " -0.207 2.00e-02 2.50e+03 pdb=" O2' 2MG A 966 " 0.874 2.00e-02 2.50e+03 pdb=" C1' 2MG A 966 " 0.206 2.00e-02 2.50e+03 pdb=" N9 2MG A 966 " -0.862 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A 967 " 0.039 2.00e-02 2.50e+03 5.51e-01 6.84e+03 pdb=" C4' 5MC A 967 " 0.415 2.00e-02 2.50e+03 pdb=" O4' 5MC A 967 " 0.631 2.00e-02 2.50e+03 pdb=" C3' 5MC A 967 " -0.627 2.00e-02 2.50e+03 pdb=" O3' 5MC A 967 " -0.514 2.00e-02 2.50e+03 pdb=" C2' 5MC A 967 " -0.219 2.00e-02 2.50e+03 pdb=" O2' 5MC A 967 " 0.857 2.00e-02 2.50e+03 pdb=" C1' 5MC A 967 " 0.236 2.00e-02 2.50e+03 pdb=" N1 5MC A 967 " -0.818 2.00e-02 2.50e+03 ... (remaining 1678 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.41: 126 2.41 - 3.09: 12460 3.09 - 3.77: 42338 3.77 - 4.46: 64588 4.46 - 5.14: 87703 Nonbonded interactions: 207215 Sorted by model distance: nonbonded pdb=" OP1 C A 980 " pdb="MG MG A1618 " model vdw 1.726 2.170 nonbonded pdb=" OP1 U A1224 " pdb="MG MG A1624 " model vdw 1.831 2.170 nonbonded pdb=" O6 G A1370 " pdb="MG MG A1607 " model vdw 1.848 2.170 nonbonded pdb="MG MG A1609 " pdb=" O HOH A1722 " model vdw 1.856 2.170 nonbonded pdb=" OP1 C A1303 " pdb="MG MG A1625 " model vdw 1.877 2.170 ... (remaining 207210 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 individual isotropic 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: 8.700 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: 27.820 Check model and map are aligned: 0.240 Set scattering table: 0.170 Process input model: 65.170 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 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: 0.020 Load rotamer database and sin/cos tables:13.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 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 : 0.012 0.499 18881 Z= 0.749 Angle : 1.534 26.143 27939 Z= 0.950 Chirality : 0.144 4.913 3527 Planarity : 0.031 0.591 1681 Dihedral : 14.843 168.365 8699 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.03 % Favored : 96.84 % Rotamer: Outliers : 0.71 % Allowed : 4.13 % Favored : 95.16 % 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: -1.46 (0.24), residues: 824 helix: -1.01 (0.22), residues: 352 sheet: -0.44 (0.39), residues: 147 loop : -0.95 (0.30), residues: 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 198 time to evaluate : 1.318 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 200 average time/residue: 1.9235 time to fit residues: 417.3681 Evaluate side-chains 141 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.4633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 103 optimal weight: 0.0970 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 69 HIS C 102 ASN C 139 GLN C 190 HIS I 75 GLN I 81 HIS I 126 GLN J 56 HIS J 58 ASN J 64 GLN N 60 GLN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 83 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18881 Z= 0.166 Angle : 0.721 21.782 27939 Z= 0.394 Chirality : 0.050 1.961 3527 Planarity : 0.007 0.127 1681 Dihedral : 13.669 162.784 6990 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.82 % Favored : 98.06 % Rotamer: Outliers : 1.71 % Allowed : 11.38 % Favored : 86.91 % 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 (0.28), residues: 824 helix: 1.22 (0.27), residues: 354 sheet: 0.10 (0.38), residues: 150 loop : -0.09 (0.33), residues: 320 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 1.129 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 167 average time/residue: 1.8378 time to fit residues: 333.9483 Evaluate side-chains 136 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.3107 time to fit residues: 2.8718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.2980 chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 100 GLN C 102 ASN C 139 GLN G 97 ASN I 75 GLN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18881 Z= 0.216 Angle : 0.776 22.934 27939 Z= 0.412 Chirality : 0.052 2.027 3527 Planarity : 0.008 0.134 1681 Dihedral : 13.791 163.367 6990 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.58 % Favored : 98.30 % Rotamer: Outliers : 1.42 % Allowed : 13.94 % Favored : 84.64 % 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: 1.06 (0.28), residues: 824 helix: 1.35 (0.27), residues: 363 sheet: 0.53 (0.38), residues: 146 loop : 0.18 (0.35), residues: 315 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 1.132 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 137 average time/residue: 1.7840 time to fit residues: 267.4370 Evaluate side-chains 131 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 1.291 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 1.2371 time to fit residues: 2.8092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 0.0980 chunk 80 optimal weight: 1.9990 chunk 120 optimal weight: 0.0970 chunk 127 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 ASN C 100 GLN C 102 ASN C 139 GLN G 97 ASN I 75 GLN M 14 HIS ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18881 Z= 0.145 Angle : 0.685 23.325 27939 Z= 0.372 Chirality : 0.049 1.963 3527 Planarity : 0.007 0.128 1681 Dihedral : 13.608 163.554 6990 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.58 % Favored : 98.30 % Rotamer: Outliers : 1.85 % Allowed : 14.08 % Favored : 84.07 % 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: 1.52 (0.29), residues: 824 helix: 1.77 (0.27), residues: 362 sheet: 0.79 (0.39), residues: 146 loop : 0.34 (0.35), residues: 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 1.221 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 141 average time/residue: 1.8421 time to fit residues: 283.6017 Evaluate side-chains 131 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 125 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.3743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 65 optimal weight: 0.0060 chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 GLN C 102 ASN C 139 GLN I 75 GLN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18881 Z= 0.292 Angle : 0.869 22.456 27939 Z= 0.451 Chirality : 0.056 2.089 3527 Planarity : 0.008 0.138 1681 Dihedral : 13.917 161.824 6990 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.70 % Favored : 98.18 % Rotamer: Outliers : 1.99 % Allowed : 15.36 % Favored : 82.65 % 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: 1.03 (0.28), residues: 824 helix: 1.18 (0.27), residues: 364 sheet: 0.69 (0.38), residues: 150 loop : 0.25 (0.35), residues: 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 1.347 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 137 average time/residue: 1.8252 time to fit residues: 273.3937 Evaluate side-chains 128 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 1.192 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.2030 time to fit residues: 1.7096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 0.2980 chunk 123 optimal weight: 4.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 ASN C 100 GLN C 102 ASN C 139 GLN I 75 GLN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 18881 Z= 0.411 Angle : 1.032 21.816 27939 Z= 0.520 Chirality : 0.062 2.186 3527 Planarity : 0.010 0.143 1681 Dihedral : 14.187 161.002 6990 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.91 % Favored : 96.97 % Rotamer: Outliers : 2.28 % Allowed : 14.51 % Favored : 83.21 % 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: 0.43 (0.28), residues: 824 helix: 0.63 (0.27), residues: 358 sheet: 0.49 (0.38), residues: 152 loop : -0.03 (0.34), residues: 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 1.343 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 142 average time/residue: 1.8718 time to fit residues: 290.2276 Evaluate side-chains 131 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.225 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.1699 time to fit residues: 1.7457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 ASN C 100 GLN C 102 ASN C 139 GLN I 75 GLN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18881 Z= 0.201 Angle : 0.746 22.776 27939 Z= 0.400 Chirality : 0.051 2.025 3527 Planarity : 0.007 0.133 1681 Dihedral : 13.751 162.145 6990 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.82 % Favored : 98.06 % Rotamer: Outliers : 1.71 % Allowed : 15.22 % Favored : 83.07 % 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: 1.06 (0.29), residues: 824 helix: 1.25 (0.27), residues: 363 sheet: 0.58 (0.37), residues: 153 loop : 0.28 (0.36), residues: 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 1.307 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 132 average time/residue: 1.8685 time to fit residues: 268.7500 Evaluate side-chains 129 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 1.281 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.1671 time to fit residues: 1.7089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 0.4980 chunk 121 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 GLN C 102 ASN C 139 GLN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18881 Z= 0.190 Angle : 0.737 22.985 27939 Z= 0.396 Chirality : 0.051 2.009 3527 Planarity : 0.007 0.132 1681 Dihedral : 13.732 162.257 6990 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.06 % Favored : 97.82 % Rotamer: Outliers : 2.13 % Allowed : 14.94 % Favored : 82.93 % 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: 1.19 (0.29), residues: 824 helix: 1.38 (0.28), residues: 363 sheet: 0.64 (0.37), residues: 153 loop : 0.33 (0.35), residues: 308 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 1.168 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 134 average time/residue: 2.0335 time to fit residues: 298.0107 Evaluate side-chains 131 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 1.307 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.1786 time to fit residues: 1.8050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 0.0770 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 ASN C 100 GLN C 102 ASN C 139 GLN I 75 GLN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18881 Z= 0.175 Angle : 0.723 23.087 27939 Z= 0.391 Chirality : 0.050 1.992 3527 Planarity : 0.007 0.132 1681 Dihedral : 13.726 162.411 6990 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.94 % Favored : 97.94 % Rotamer: Outliers : 1.56 % Allowed : 16.07 % Favored : 82.36 % 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: 1.25 (0.29), residues: 824 helix: 1.48 (0.28), residues: 357 sheet: 0.65 (0.38), residues: 153 loop : 0.31 (0.35), residues: 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 1.259 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 134 average time/residue: 1.9877 time to fit residues: 290.5525 Evaluate side-chains 131 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.2863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.3980 chunk 87 optimal weight: 0.0870 chunk 131 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 GLN C 102 ASN C 139 GLN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18881 Z= 0.168 Angle : 0.716 23.117 27939 Z= 0.388 Chirality : 0.050 1.989 3527 Planarity : 0.007 0.131 1681 Dihedral : 13.715 162.512 6990 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.06 % Favored : 97.82 % Rotamer: Outliers : 1.56 % Allowed : 16.36 % Favored : 82.08 % 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: 1.28 (0.29), residues: 824 helix: 1.45 (0.28), residues: 363 sheet: 0.66 (0.38), residues: 153 loop : 0.38 (0.35), residues: 308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.338 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 130 average time/residue: 1.8503 time to fit residues: 262.2329 Evaluate side-chains 127 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.207 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.3582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 GLN C 102 ASN C 139 GLN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.164485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.132216 restraints weight = 16322.109| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 0.56 r_work: 0.3449 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18881 Z= 0.216 Angle : 0.768 22.829 27939 Z= 0.409 Chirality : 0.052 2.031 3527 Planarity : 0.007 0.134 1681 Dihedral : 13.752 162.959 6990 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.18 % Favored : 97.69 % Rotamer: Outliers : 1.56 % Allowed : 15.93 % Favored : 82.50 % 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: 1.22 (0.29), residues: 824 helix: 1.33 (0.27), residues: 363 sheet: 0.77 (0.38), residues: 151 loop : 0.37 (0.35), residues: 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6178.50 seconds wall clock time: 111 minutes 23.34 seconds (6683.34 seconds total)