Starting phenix.real_space_refine on Thu Aug 6 04:34:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqk_34028/08_2026/7yqk_34028.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqk_34028/08_2026/7yqk_34028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yqk_34028/08_2026/7yqk_34028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqk_34028/08_2026/7yqk_34028.map" model { file = "/net/cci-nas-00/data/ceres_data/7yqk_34028/08_2026/7yqk_34028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqk_34028/08_2026/7yqk_34028.cif" } resolution = 3.38 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 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: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 20 5.16 5 C 7742 2.51 5 N 2559 2.21 5 O 3136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13745 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 857 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 745 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 842 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 734 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "O" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 597 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "K" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 140 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 948 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 115} Time building chain proxies: 3.39, per 1000 atoms: 0.25 Number of scatterers: 13745 At special positions: 0 Unit cell: (115.56, 107, 114.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 288 15.00 O 3136 8.00 N 2559 7.00 C 7742 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 546.4 milliseconds 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 13 sheets defined 56.6% alpha, 7.3% beta 132 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.809A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.611A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.575A pdb=" N ALA B 89 " --> pdb=" O ASP B 85 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.658A pdb=" N ARG C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.486A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.720A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.580A pdb=" N TYR D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS D 43 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.930A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.612A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.724A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.550A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.600A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.974A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.625A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.703A pdb=" N HIS G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS G 36 " --> pdb=" O ARG G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.372A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.792A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 4.016A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.599A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.575A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 4.088A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 32 Processing helix chain 'O' and resid 37 through 41 Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'N' and resid 1528 through 1530 No H-bonds generated for 'chain 'N' and resid 1528 through 1530' Processing helix chain 'N' and resid 1589 through 1594 Processing helix chain 'N' and resid 1596 through 1601 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.971A 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 removed outlier: 6.384A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.640A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (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 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.037A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.210A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'O' and resid 13 through 15 removed outlier: 3.524A pdb=" N ILE O 3 " --> pdb=" O LEU O 15 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 1502 through 1503 Processing sheet with id=AB3, first strand: chain 'N' and resid 1506 through 1509 removed outlier: 6.913A pdb=" N ILE N1506 " --> pdb=" O LEU N1518 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU N1518 " --> pdb=" O ILE N1506 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG N1508 " --> pdb=" O LYS N1516 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU N1517 " --> pdb=" O CYS N1525 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS N1525 " --> pdb=" O LEU N1517 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 1577 through 1582 removed outlier: 5.899A pdb=" N GLU N1567 " --> pdb=" O LYS N1563 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LYS N1563 " --> pdb=" O GLU N1567 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR N1569 " --> pdb=" O HIS N1561 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N HIS N1561 " --> pdb=" O TYR N1569 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N SER N1571 " --> pdb=" O LYS N1559 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER N1554 " --> pdb=" O ALA N1546 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 335 hydrogen bonds 662 hydrogen bond angles 0 basepair planarities 132 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 1.28 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: 3236 1.33 - 1.45: 4265 1.45 - 1.57: 6465 1.57 - 1.69: 576 1.69 - 1.81: 32 Bond restraints: 14574 Sorted by residual: bond pdb=" C3' DG J 23 " pdb=" C2' DG J 23 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DG J -21 " pdb=" C2' DG J -21 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DG I 2 " pdb=" C2' DG I 2 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.94e+00 bond pdb=" C3' DG I 20 " pdb=" C2' DG I 20 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.50e+00 ... (remaining 14569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 19653 1.61 - 3.22: 1175 3.22 - 4.84: 64 4.84 - 6.45: 14 6.45 - 8.06: 4 Bond angle restraints: 20910 Sorted by residual: angle pdb=" O4' DT I -26 " pdb=" C4' DT I -26 " pdb=" C3' DT I -26 " ideal model delta sigma weight residual 106.00 102.97 3.03 6.00e-01 2.78e+00 2.56e+01 angle pdb=" N3 DT I -71 " pdb=" C4 DT I -71 " pdb=" O4 DT I -71 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" O4' DG I 47 " pdb=" C4' DG I 47 " pdb=" C3' DG I 47 " ideal model delta sigma weight residual 106.00 103.37 2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT J -32 " pdb=" C4 DT J -32 " pdb=" O4 DT J -32 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT I 38 " pdb=" C4 DT I 38 " pdb=" O4 DT I 38 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 ... (remaining 20905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.42: 6498 31.42 - 62.83: 1499 62.83 - 94.25: 34 94.25 - 125.66: 1 125.66 - 157.08: 2 Dihedral angle restraints: 8034 sinusoidal: 5188 harmonic: 2846 Sorted by residual: dihedral pdb=" CA ASP K1616 " pdb=" C ASP K1616 " pdb=" N ILE K1617 " pdb=" CA ILE K1617 " ideal model delta harmonic sigma weight residual -180.00 -142.46 -37.54 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CA SER K1618 " pdb=" C SER K1618 " pdb=" N LEU K1619 " pdb=" CA LEU K1619 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA LYS G 13 " pdb=" C LYS G 13 " pdb=" N ALA G 14 " pdb=" CA ALA G 14 " ideal model delta harmonic sigma weight residual 180.00 158.82 21.18 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 8031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1281 0.032 - 0.064: 662 0.064 - 0.096: 269 0.096 - 0.128: 140 0.128 - 0.160: 19 Chirality restraints: 2371 Sorted by residual: chirality pdb=" CB ILE O 36 " pdb=" CA ILE O 36 " pdb=" CG1 ILE O 36 " pdb=" CG2 ILE O 36 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CA GLU B 63 " pdb=" N GLU B 63 " pdb=" C GLU B 63 " pdb=" CB GLU B 63 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA GLN A 125 " pdb=" N GLN A 125 " pdb=" C GLN A 125 " pdb=" CB GLN A 125 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.01e-01 ... (remaining 2368 not shown) Planarity restraints: 1646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 116 " 0.042 5.00e-02 4.00e+02 6.29e-02 6.32e+00 pdb=" N PRO C 117 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 117 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 117 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO G 80 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 93 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.94e+00 pdb=" C GLN A 93 " 0.034 2.00e-02 2.50e+03 pdb=" O GLN A 93 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 94 " -0.012 2.00e-02 2.50e+03 ... (remaining 1643 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 445 2.66 - 3.22: 12603 3.22 - 3.78: 25550 3.78 - 4.34: 32935 4.34 - 4.90: 46313 Nonbonded interactions: 117846 Sorted by model distance: nonbonded pdb=" N2 DG I 52 " pdb=" O2 DC J -52 " model vdw 2.105 2.496 nonbonded pdb=" O2 DC I -38 " pdb=" N2 DG J 38 " model vdw 2.130 2.496 nonbonded pdb=" OG SER C 18 " pdb=" O LEU C 23 " model vdw 2.166 3.040 nonbonded pdb=" O HIS H 109 " pdb=" OG SER H 112 " model vdw 2.193 3.040 nonbonded pdb=" OE1 GLU A 50 " pdb=" NH1 ARG B 39 " model vdw 2.203 3.120 ... (remaining 117841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 37 through 134) selection = (chain 'E' and resid 37 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = (chain 'C' and (resid 10 through 118 or (resid 119 through 120 and (name N or na \ me CA or name C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = (chain 'D' and ((resid 30 through 31 and (name N or name CA or name C or name O \ or name CB )) or resid 32 through 124)) 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=0.00 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: 1.560 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.380 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 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 : 0.006 0.059 14574 Z= 0.523 Angle : 0.789 8.061 20910 Z= 0.646 Chirality : 0.048 0.160 2371 Planarity : 0.004 0.063 1646 Dihedral : 26.061 157.077 6204 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.26), residues: 965 helix: 0.29 (0.23), residues: 537 sheet: -1.25 (0.75), residues: 34 loop : -1.41 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 79 TYR 0.032 0.002 TYR F 88 PHE 0.023 0.002 PHE C 25 TRP 0.001 0.000 TRP N1495 HIS 0.007 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.52 (14574) covalent geometry : angle 0.78888 / 0.65 (20910) hydrogen bonds : bond 0.17655 / 11.68 ( 743) hydrogen bonds : angle 6.41787 / 4.56 ( 1853) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 THR cc_start: 0.8638 (p) cc_final: 0.8309 (p) REVERT: A 97 GLU cc_start: 0.8316 (mp0) cc_final: 0.7965 (mp0) REVERT: A 125 GLN cc_start: 0.9165 (pm20) cc_final: 0.8950 (pm20) REVERT: B 59 LYS cc_start: 0.9146 (ttpp) cc_final: 0.8771 (ttmt) REVERT: B 84 MET cc_start: 0.8761 (mmt) cc_final: 0.8325 (mmt) REVERT: B 85 ASP cc_start: 0.8968 (m-30) cc_final: 0.8534 (m-30) REVERT: B 88 TYR cc_start: 0.8994 (m-80) cc_final: 0.8735 (m-80) REVERT: C 64 GLU cc_start: 0.8797 (tp30) cc_final: 0.8328 (tp30) REVERT: C 104 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8751 (mm-40) REVERT: E 64 LYS cc_start: 0.9038 (mmmm) cc_final: 0.8663 (mmmm) REVERT: E 79 LYS cc_start: 0.8648 (tttm) cc_final: 0.8443 (ttmm) REVERT: E 80 THR cc_start: 0.9455 (m) cc_final: 0.9219 (t) REVERT: F 44 LYS cc_start: 0.9162 (ttmt) cc_final: 0.8633 (ttmt) REVERT: F 85 ASP cc_start: 0.9108 (m-30) cc_final: 0.8868 (m-30) REVERT: G 72 ASP cc_start: 0.9093 (m-30) cc_final: 0.8778 (m-30) REVERT: H 68 ASP cc_start: 0.9011 (t0) cc_final: 0.8802 (t0) REVERT: H 83 TYR cc_start: 0.8367 (m-80) cc_final: 0.7807 (m-80) REVERT: O 62 GLN cc_start: 0.8971 (mm110) cc_final: 0.8558 (mm110) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1259 time to fit residues: 45.5634 Evaluate side-chains 223 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 30.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN O 2 GLN ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.054343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.036016 restraints weight = 65888.011| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 3.33 r_work: 0.2504 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14574 Z= 0.197 Angle : 0.706 7.869 20910 Z= 0.407 Chirality : 0.045 0.255 2371 Planarity : 0.005 0.053 1646 Dihedral : 29.819 158.640 4264 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.56 % Allowed : 10.00 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.27), residues: 965 helix: 0.75 (0.22), residues: 558 sheet: -1.33 (0.67), residues: 39 loop : -1.37 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 67 TYR 0.034 0.002 TYR H 83 PHE 0.017 0.002 PHE E 67 TRP 0.002 0.001 TRP N1495 HIS 0.007 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.20 (14574) covalent geometry : angle 0.70593 / 0.41 (20910) hydrogen bonds : bond 0.06270 / 4.23 ( 743) hydrogen bonds : angle 4.19025 / 2.98 ( 1853) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 245 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8627 (pp20) cc_final: 0.8413 (tm-30) REVERT: A 106 ASP cc_start: 0.9001 (m-30) cc_final: 0.8562 (m-30) REVERT: B 53 GLU cc_start: 0.8352 (pm20) cc_final: 0.8057 (pm20) REVERT: B 59 LYS cc_start: 0.9159 (ttpp) cc_final: 0.8824 (ttmt) REVERT: B 74 GLU cc_start: 0.9323 (mm-30) cc_final: 0.9120 (mm-30) REVERT: B 84 MET cc_start: 0.9271 (mmt) cc_final: 0.8771 (mmt) REVERT: B 85 ASP cc_start: 0.9155 (m-30) cc_final: 0.8756 (m-30) REVERT: B 88 TYR cc_start: 0.9202 (m-80) cc_final: 0.8971 (m-80) REVERT: C 56 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8705 (mm-30) REVERT: C 64 GLU cc_start: 0.9192 (tp30) cc_final: 0.8730 (tp30) REVERT: D 71 GLU cc_start: 0.9406 (mm-30) cc_final: 0.9083 (tp30) REVERT: D 76 GLU cc_start: 0.9207 (tp30) cc_final: 0.8850 (tp30) REVERT: D 79 ARG cc_start: 0.8760 (mpp-170) cc_final: 0.8268 (mtm-85) REVERT: E 64 LYS cc_start: 0.9198 (mmmm) cc_final: 0.8870 (mmmm) REVERT: E 80 THR cc_start: 0.9611 (m) cc_final: 0.9386 (t) REVERT: E 125 GLN cc_start: 0.9256 (mt0) cc_final: 0.9042 (mt0) REVERT: F 85 ASP cc_start: 0.9397 (m-30) cc_final: 0.9158 (m-30) REVERT: G 64 GLU cc_start: 0.9487 (tt0) cc_final: 0.8982 (tm-30) REVERT: G 72 ASP cc_start: 0.9295 (m-30) cc_final: 0.9040 (m-30) REVERT: G 92 GLU cc_start: 0.8745 (tt0) cc_final: 0.7979 (tt0) REVERT: O 40 GLN cc_start: 0.8174 (mm110) cc_final: 0.7820 (mm110) REVERT: O 62 GLN cc_start: 0.9149 (mm110) cc_final: 0.8720 (mm110) REVERT: O 69 LEU cc_start: 0.9588 (tp) cc_final: 0.9353 (pp) REVERT: K 1626 LYS cc_start: 0.7829 (tptt) cc_final: 0.7220 (tptt) outliers start: 21 outliers final: 14 residues processed: 254 average time/residue: 0.1252 time to fit residues: 45.0361 Evaluate side-chains 232 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 71 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 0.0060 chunk 55 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 67 optimal weight: 0.0770 chunk 105 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.054899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.036247 restraints weight = 66393.701| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 3.42 r_work: 0.2517 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14574 Z= 0.153 Angle : 0.654 8.825 20910 Z= 0.381 Chirality : 0.044 0.265 2371 Planarity : 0.004 0.056 1646 Dihedral : 29.850 156.918 4264 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.56 % Allowed : 12.56 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.27), residues: 965 helix: 1.04 (0.22), residues: 557 sheet: -0.82 (0.77), residues: 29 loop : -1.30 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K1629 TYR 0.025 0.002 TYR H 83 PHE 0.012 0.001 PHE E 67 TRP 0.004 0.001 TRP N1580 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (14574) covalent geometry : angle 0.65391 / 0.38 (20910) hydrogen bonds : bond 0.05267 / 3.62 ( 743) hydrogen bonds : angle 3.80644 / 2.68 ( 1853) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 252 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9406 (mt-10) cc_final: 0.9056 (mt-10) REVERT: A 79 LYS cc_start: 0.9128 (mtpp) cc_final: 0.8845 (mtpt) REVERT: A 93 GLN cc_start: 0.9405 (tt0) cc_final: 0.9190 (tt0) REVERT: A 97 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8618 (mp0) REVERT: A 105 GLU cc_start: 0.8663 (pp20) cc_final: 0.8346 (tm-30) REVERT: A 106 ASP cc_start: 0.9066 (m-30) cc_final: 0.8582 (m-30) REVERT: B 59 LYS cc_start: 0.9411 (ttpp) cc_final: 0.8929 (ttmt) REVERT: B 63 GLU cc_start: 0.9021 (pm20) cc_final: 0.8542 (pm20) REVERT: B 84 MET cc_start: 0.9300 (mmt) cc_final: 0.8902 (mmt) REVERT: B 85 ASP cc_start: 0.9202 (m-30) cc_final: 0.8813 (m-30) REVERT: C 56 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8699 (mm-30) REVERT: C 64 GLU cc_start: 0.9232 (tp30) cc_final: 0.8759 (tp30) REVERT: D 34 LYS cc_start: 0.8762 (mmtm) cc_final: 0.8139 (mmtt) REVERT: D 71 GLU cc_start: 0.9431 (mm-30) cc_final: 0.9122 (tp30) REVERT: E 64 LYS cc_start: 0.9185 (mmmm) cc_final: 0.8871 (mmmm) REVERT: E 125 GLN cc_start: 0.9266 (mt0) cc_final: 0.8992 (mt0) REVERT: F 52 GLU cc_start: 0.8882 (mp0) cc_final: 0.8624 (pm20) REVERT: F 85 ASP cc_start: 0.9428 (m-30) cc_final: 0.9205 (m-30) REVERT: G 72 ASP cc_start: 0.9256 (m-30) cc_final: 0.8954 (m-30) REVERT: H 105 GLU cc_start: 0.9056 (pm20) cc_final: 0.8753 (pm20) REVERT: O 40 GLN cc_start: 0.8207 (mm110) cc_final: 0.7868 (mm110) REVERT: O 62 GLN cc_start: 0.9152 (mm110) cc_final: 0.8720 (mm110) outliers start: 21 outliers final: 12 residues processed: 262 average time/residue: 0.1189 time to fit residues: 44.3275 Evaluate side-chains 240 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 227 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 31 GLN Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN ** O 41 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 = 0.3292 r_free = 0.3292 target = 0.053624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.035202 restraints weight = 66167.222| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 3.33 r_work: 0.2478 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14574 Z= 0.225 Angle : 0.689 7.442 20910 Z= 0.391 Chirality : 0.044 0.282 2371 Planarity : 0.004 0.059 1646 Dihedral : 30.034 158.916 4264 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.90 % Allowed : 13.90 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.27), residues: 965 helix: 1.28 (0.22), residues: 556 sheet: -0.61 (0.95), residues: 24 loop : -1.30 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 31 TYR 0.037 0.002 TYR B 88 PHE 0.010 0.001 PHE E 67 TRP 0.004 0.001 TRP N1580 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.22 (14574) covalent geometry : angle 0.68922 / 0.39 (20910) hydrogen bonds : bond 0.05428 / 3.66 ( 743) hydrogen bonds : angle 3.77637 / 2.69 ( 1853) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8406 (tm-30) REVERT: A 125 GLN cc_start: 0.9247 (OUTLIER) cc_final: 0.8984 (pm20) REVERT: B 59 LYS cc_start: 0.9354 (ttpp) cc_final: 0.8995 (ttmt) REVERT: B 63 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8682 (pm20) REVERT: B 84 MET cc_start: 0.9279 (mmt) cc_final: 0.8856 (mmt) REVERT: B 85 ASP cc_start: 0.9195 (m-30) cc_final: 0.8920 (m-30) REVERT: B 88 TYR cc_start: 0.9240 (m-80) cc_final: 0.8872 (m-80) REVERT: C 56 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8726 (mm-30) REVERT: D 71 GLU cc_start: 0.9417 (mm-30) cc_final: 0.9193 (tp30) REVERT: F 85 ASP cc_start: 0.9405 (m-30) cc_final: 0.9164 (m-30) REVERT: G 72 ASP cc_start: 0.9241 (m-30) cc_final: 0.8907 (m-30) REVERT: G 92 GLU cc_start: 0.8545 (tt0) cc_final: 0.7996 (tt0) REVERT: H 83 TYR cc_start: 0.8469 (m-80) cc_final: 0.8198 (m-80) REVERT: H 105 GLU cc_start: 0.9051 (pm20) cc_final: 0.8770 (pm20) REVERT: O 40 GLN cc_start: 0.8222 (mm110) cc_final: 0.7870 (mm110) outliers start: 32 outliers final: 23 residues processed: 234 average time/residue: 0.1087 time to fit residues: 35.9015 Evaluate side-chains 239 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 31 HIS Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 4 PHE Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 31 GLN Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 71 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 27 optimal weight: 9.9990 chunk 102 optimal weight: 0.2980 chunk 78 optimal weight: 20.0000 chunk 119 optimal weight: 30.0000 chunk 103 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 88 optimal weight: 30.0000 overall best weight: 4.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.052696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.034186 restraints weight = 67463.767| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 3.27 r_work: 0.2440 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 14574 Z= 0.291 Angle : 0.741 8.162 20910 Z= 0.411 Chirality : 0.046 0.292 2371 Planarity : 0.004 0.058 1646 Dihedral : 30.221 158.800 4264 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.15 % Allowed : 15.73 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.27), residues: 965 helix: 1.33 (0.22), residues: 556 sheet: -0.66 (0.94), residues: 24 loop : -1.30 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K1629 TYR 0.029 0.002 TYR B 88 PHE 0.012 0.001 PHE E 67 TRP 0.004 0.001 TRP N1580 HIS 0.012 0.002 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.29 (14574) covalent geometry : angle 0.74075 / 0.41 (20910) hydrogen bonds : bond 0.05748 / 3.83 ( 743) hydrogen bonds : angle 3.82788 / 2.72 ( 1853) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 218 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8968 (m-30) cc_final: 0.8636 (m-30) REVERT: B 84 MET cc_start: 0.9334 (mmt) cc_final: 0.8988 (mmt) REVERT: B 85 ASP cc_start: 0.9204 (m-30) cc_final: 0.8962 (m-30) REVERT: B 88 TYR cc_start: 0.9387 (m-80) cc_final: 0.9117 (m-80) REVERT: C 56 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8762 (mm-30) REVERT: D 47 GLN cc_start: 0.9578 (mm-40) cc_final: 0.9369 (mm-40) REVERT: D 71 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9203 (tp30) REVERT: F 52 GLU cc_start: 0.8938 (mp0) cc_final: 0.8668 (pm20) REVERT: F 85 ASP cc_start: 0.9446 (m-30) cc_final: 0.9210 (m-30) REVERT: G 72 ASP cc_start: 0.9178 (m-30) cc_final: 0.8848 (m-30) REVERT: O 40 GLN cc_start: 0.8367 (mm110) cc_final: 0.8010 (mm110) outliers start: 34 outliers final: 24 residues processed: 232 average time/residue: 0.1035 time to fit residues: 33.8284 Evaluate side-chains 230 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 31 HIS Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 4 PHE Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 31 GLN Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 99 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 27 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 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 = 0.3282 r_free = 0.3282 target = 0.053258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.034719 restraints weight = 66444.251| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 3.30 r_work: 0.2455 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14574 Z= 0.197 Angle : 0.692 8.048 20910 Z= 0.391 Chirality : 0.044 0.291 2371 Planarity : 0.004 0.058 1646 Dihedral : 30.185 158.251 4264 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.78 % Allowed : 16.95 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.27), residues: 965 helix: 1.41 (0.22), residues: 556 sheet: -0.63 (0.95), residues: 24 loop : -1.22 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 79 TYR 0.024 0.002 TYR H 83 PHE 0.010 0.001 PHE E 67 TRP 0.003 0.001 TRP N1580 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.20 (14574) covalent geometry : angle 0.69182 / 0.39 (20910) hydrogen bonds : bond 0.04972 / 3.37 ( 743) hydrogen bonds : angle 3.64302 / 2.59 ( 1853) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9123 (m-30) cc_final: 0.8860 (m-30) REVERT: A 125 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8926 (pm20) REVERT: B 84 MET cc_start: 0.9307 (mmt) cc_final: 0.8998 (mmt) REVERT: B 85 ASP cc_start: 0.9214 (m-30) cc_final: 0.8957 (m-30) REVERT: B 88 TYR cc_start: 0.9412 (m-80) cc_final: 0.9162 (m-80) REVERT: C 56 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8737 (mm-30) REVERT: D 47 GLN cc_start: 0.9578 (mm-40) cc_final: 0.9360 (mm-40) REVERT: F 52 GLU cc_start: 0.8921 (mp0) cc_final: 0.8668 (pm20) REVERT: F 85 ASP cc_start: 0.9426 (m-30) cc_final: 0.9201 (m-30) REVERT: G 31 HIS cc_start: 0.9040 (OUTLIER) cc_final: 0.8579 (m-70) REVERT: G 72 ASP cc_start: 0.9163 (m-30) cc_final: 0.8844 (m-30) REVERT: O 40 GLN cc_start: 0.8353 (mm110) cc_final: 0.8031 (mm110) outliers start: 31 outliers final: 22 residues processed: 244 average time/residue: 0.1100 time to fit residues: 37.6484 Evaluate side-chains 241 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 31 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 4 PHE Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 31 GLN Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 115 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 119 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 chunk 95 optimal weight: 20.0000 chunk 45 optimal weight: 0.2980 chunk 39 optimal weight: 0.4980 chunk 87 optimal weight: 30.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.053507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.034992 restraints weight = 66856.715| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 3.38 r_work: 0.2463 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14574 Z= 0.168 Angle : 0.693 9.512 20910 Z= 0.391 Chirality : 0.044 0.291 2371 Planarity : 0.004 0.058 1646 Dihedral : 30.141 159.146 4264 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.17 % Allowed : 18.41 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.27), residues: 965 helix: 1.39 (0.22), residues: 555 sheet: -0.55 (0.96), residues: 24 loop : -1.22 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K1629 TYR 0.033 0.002 TYR D 83 PHE 0.010 0.001 PHE E 67 TRP 0.003 0.001 TRP N1580 HIS 0.005 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (14574) covalent geometry : angle 0.69347 / 0.39 (20910) hydrogen bonds : bond 0.04806 / 3.27 ( 743) hydrogen bonds : angle 3.58945 / 2.54 ( 1853) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9076 (m-30) cc_final: 0.8849 (m-30) REVERT: A 125 GLN cc_start: 0.9268 (OUTLIER) cc_final: 0.8908 (pm20) REVERT: B 84 MET cc_start: 0.9289 (mmt) cc_final: 0.9028 (mmt) REVERT: B 85 ASP cc_start: 0.9218 (m-30) cc_final: 0.8962 (m-30) REVERT: C 56 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8732 (mm-30) REVERT: D 47 GLN cc_start: 0.9563 (mm-40) cc_final: 0.9348 (mm-40) REVERT: E 73 GLU cc_start: 0.9522 (tt0) cc_final: 0.9245 (tt0) REVERT: F 52 GLU cc_start: 0.8977 (mp0) cc_final: 0.8718 (pm20) REVERT: F 85 ASP cc_start: 0.9416 (m-30) cc_final: 0.9195 (m-30) REVERT: G 31 HIS cc_start: 0.8995 (OUTLIER) cc_final: 0.8510 (m-70) REVERT: G 72 ASP cc_start: 0.9189 (m-30) cc_final: 0.8870 (m-30) REVERT: H 105 GLU cc_start: 0.8978 (pm20) cc_final: 0.8725 (pm20) REVERT: O 40 GLN cc_start: 0.8348 (mm110) cc_final: 0.8044 (mm110) REVERT: O 62 GLN cc_start: 0.9216 (mm110) cc_final: 0.8840 (mm110) outliers start: 26 outliers final: 18 residues processed: 241 average time/residue: 0.1173 time to fit residues: 40.0934 Evaluate side-chains 240 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 31 HIS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 4 PHE Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 31 GLN Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 106 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 111 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.053872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.035393 restraints weight = 66638.967| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 3.33 r_work: 0.2477 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14574 Z= 0.164 Angle : 0.695 9.466 20910 Z= 0.391 Chirality : 0.044 0.294 2371 Planarity : 0.004 0.059 1646 Dihedral : 30.108 160.247 4264 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.17 % Allowed : 19.15 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.27), residues: 965 helix: 1.36 (0.22), residues: 556 sheet: -0.41 (1.00), residues: 24 loop : -1.19 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K1629 TYR 0.040 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 TRP 0.003 0.001 TRP N1580 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (14574) covalent geometry : angle 0.69496 / 0.39 (20910) hydrogen bonds : bond 0.04717 / 3.22 ( 743) hydrogen bonds : angle 3.56728 / 2.52 ( 1853) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8977 (ttmm) cc_final: 0.8636 (ttmm) REVERT: A 106 ASP cc_start: 0.9097 (m-30) cc_final: 0.8846 (m-30) REVERT: A 125 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.8886 (pm20) REVERT: B 84 MET cc_start: 0.9265 (mmt) cc_final: 0.8839 (mmt) REVERT: B 88 TYR cc_start: 0.9229 (m-80) cc_final: 0.8824 (m-80) REVERT: D 47 GLN cc_start: 0.9552 (mm-40) cc_final: 0.9331 (mm-40) REVERT: E 73 GLU cc_start: 0.9514 (tt0) cc_final: 0.9243 (tt0) REVERT: F 52 GLU cc_start: 0.8958 (mp0) cc_final: 0.8679 (pm20) REVERT: F 85 ASP cc_start: 0.9407 (m-30) cc_final: 0.9190 (m-30) REVERT: G 72 ASP cc_start: 0.9162 (m-30) cc_final: 0.8845 (m-30) REVERT: H 105 GLU cc_start: 0.8970 (pm20) cc_final: 0.8749 (pm20) REVERT: O 40 GLN cc_start: 0.8263 (mm110) cc_final: 0.8009 (mm110) REVERT: O 62 GLN cc_start: 0.9198 (mm110) cc_final: 0.8820 (mm110) REVERT: K 1629 ARG cc_start: 0.5308 (mpt-90) cc_final: 0.5059 (mpt-90) outliers start: 26 outliers final: 18 residues processed: 244 average time/residue: 0.1209 time to fit residues: 41.5731 Evaluate side-chains 244 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 4 PHE Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 31 GLN Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 110 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 0.0020 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.054140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.035612 restraints weight = 66842.714| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 3.36 r_work: 0.2488 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14574 Z= 0.155 Angle : 0.707 11.496 20910 Z= 0.396 Chirality : 0.044 0.302 2371 Planarity : 0.004 0.059 1646 Dihedral : 30.073 161.093 4264 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.32 % Allowed : 20.37 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.27), residues: 965 helix: 1.38 (0.22), residues: 555 sheet: -0.39 (1.07), residues: 24 loop : -1.25 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 79 TYR 0.042 0.002 TYR D 83 PHE 0.009 0.001 PHE E 67 TRP 0.003 0.001 TRP N1580 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (14574) covalent geometry : angle 0.70687 / 0.40 (20910) hydrogen bonds : bond 0.04637 / 3.17 ( 743) hydrogen bonds : angle 3.55325 / 2.50 ( 1853) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 241 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9070 (m-30) cc_final: 0.8826 (m-30) REVERT: A 125 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.8837 (pm20) REVERT: B 84 MET cc_start: 0.9277 (mmt) cc_final: 0.8815 (mmt) REVERT: B 85 ASP cc_start: 0.9187 (m-30) cc_final: 0.8861 (m-30) REVERT: B 88 TYR cc_start: 0.9150 (m-80) cc_final: 0.8659 (m-80) REVERT: C 56 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8577 (mm-30) REVERT: D 47 GLN cc_start: 0.9553 (mm-40) cc_final: 0.9314 (mm-40) REVERT: E 73 GLU cc_start: 0.9511 (tt0) cc_final: 0.9243 (tt0) REVERT: F 52 GLU cc_start: 0.8942 (mp0) cc_final: 0.8682 (pm20) REVERT: F 85 ASP cc_start: 0.9392 (m-30) cc_final: 0.9186 (m-30) REVERT: G 31 HIS cc_start: 0.9091 (OUTLIER) cc_final: 0.8578 (t-90) REVERT: G 72 ASP cc_start: 0.9166 (m-30) cc_final: 0.8859 (m-30) REVERT: H 105 GLU cc_start: 0.8975 (pm20) cc_final: 0.8755 (pm20) REVERT: O 40 GLN cc_start: 0.8218 (mm110) cc_final: 0.7908 (mm110) REVERT: O 62 GLN cc_start: 0.9207 (mm110) cc_final: 0.8827 (mm110) REVERT: K 1629 ARG cc_start: 0.5333 (mpt-90) cc_final: 0.5070 (mpt-90) outliers start: 19 outliers final: 12 residues processed: 250 average time/residue: 0.1238 time to fit residues: 43.7420 Evaluate side-chains 243 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 229 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 31 HIS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 4 PHE Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 84 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 overall best weight: 4.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** 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 = 0.3259 r_free = 0.3259 target = 0.052263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.033775 restraints weight = 67556.277| |-----------------------------------------------------------------------------| r_work (start): 0.2621 rms_B_bonded: 3.33 r_work: 0.2429 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 14574 Z= 0.308 Angle : 0.811 12.367 20910 Z= 0.439 Chirality : 0.048 0.316 2371 Planarity : 0.005 0.059 1646 Dihedral : 30.316 161.716 4264 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.20 % Allowed : 20.98 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.27), residues: 965 helix: 1.34 (0.22), residues: 556 sheet: -0.61 (0.99), residues: 24 loop : -1.32 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K1629 TYR 0.055 0.003 TYR D 83 PHE 0.009 0.002 PHE C 25 TRP 0.004 0.001 TRP N1580 HIS 0.008 0.002 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.31 (14574) covalent geometry : angle 0.81088 / 0.44 (20910) hydrogen bonds : bond 0.05850 / 3.88 ( 743) hydrogen bonds : angle 3.88328 / 2.77 ( 1853) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 220 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8825 (mp0) cc_final: 0.8594 (mp0) REVERT: A 106 ASP cc_start: 0.9062 (m-30) cc_final: 0.8814 (m-30) REVERT: A 125 GLN cc_start: 0.9289 (OUTLIER) cc_final: 0.8938 (mp10) REVERT: B 84 MET cc_start: 0.9343 (mmt) cc_final: 0.8911 (mmt) REVERT: B 85 ASP cc_start: 0.9203 (m-30) cc_final: 0.8887 (m-30) REVERT: B 88 TYR cc_start: 0.9256 (m-80) cc_final: 0.8763 (m-80) REVERT: C 56 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8618 (mm-30) REVERT: D 47 GLN cc_start: 0.9568 (mm-40) cc_final: 0.9351 (mm-40) REVERT: E 73 GLU cc_start: 0.9518 (tt0) cc_final: 0.9257 (tt0) REVERT: E 120 MET cc_start: 0.9302 (mtm) cc_final: 0.9022 (mtm) REVERT: F 85 ASP cc_start: 0.9429 (m-30) cc_final: 0.9191 (m-30) REVERT: G 72 ASP cc_start: 0.9155 (m-30) cc_final: 0.8853 (m-30) REVERT: O 40 GLN cc_start: 0.8273 (mm110) cc_final: 0.7984 (mm110) REVERT: O 62 GLN cc_start: 0.9228 (mm110) cc_final: 0.8885 (mm110) outliers start: 18 outliers final: 17 residues processed: 228 average time/residue: 0.1176 time to fit residues: 37.7392 Evaluate side-chains 235 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 4 PHE Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 78 optimal weight: 20.0000 chunk 1 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 87 optimal weight: 30.0000 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.054025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.035523 restraints weight = 67219.921| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 3.35 r_work: 0.2484 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14574 Z= 0.155 Angle : 0.731 12.205 20910 Z= 0.407 Chirality : 0.045 0.393 2371 Planarity : 0.004 0.055 1646 Dihedral : 30.117 161.188 4264 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.32 % Allowed : 22.20 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.27), residues: 965 helix: 1.40 (0.22), residues: 554 sheet: -0.75 (0.97), residues: 24 loop : -1.28 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 79 TYR 0.040 0.002 TYR D 83 PHE 0.008 0.001 PHE E 67 TRP 0.003 0.001 TRP N1580 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (14574) covalent geometry : angle 0.73109 / 0.41 (20910) hydrogen bonds : bond 0.04592 / 3.15 ( 743) hydrogen bonds : angle 3.59993 / 2.54 ( 1853) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3064.65 seconds wall clock time: 53 minutes 11.06 seconds (3191.06 seconds total)