Starting phenix.real_space_refine on Fri Jul 3 09:57:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqk_34028/07_2026/7yqk_34028.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqk_34028/07_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_34028/07_2026/7yqk_34028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqk_34028/07_2026/7yqk_34028.map" model { file = "/net/cci-nas-00/data/ceres_data/7yqk_34028/07_2026/7yqk_34028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqk_34028/07_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-dev-6108/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: 3.06, per 1000 atoms: 0.22 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: 1.14 Conformation dependent library (CDL) restraints added in 429.0 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: 1.92 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: 2.85 Time building geometry restraints manager: 1.52 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: 19663 1.61 - 3.22: 1167 3.22 - 4.84: 62 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: 1.360 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.930 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.060 ------------------------------------------------------------------------------- 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 : 0.784 8.061 20910 Z= 0.642 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 0.78440 / 0.64 (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 : 0.498 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: 0.1358 time to fit residues: 49.1552 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 : 0.391 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.054359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.036031 restraints weight = 65806.062| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 3.33 r_work: 0.2502 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14574 Z= 0.201 Angle : 0.692 7.505 20910 Z= 0.403 Chirality : 0.045 0.242 2371 Planarity : 0.005 0.053 1646 Dihedral : 29.896 159.718 4264 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.68 % Allowed : 10.00 % Favored : 87.32 % 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: -0.21 (0.27), residues: 965 helix: 0.76 (0.22), residues: 558 sheet: -1.34 (0.67), residues: 39 loop : -1.36 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 92 TYR 0.035 0.002 TYR H 83 PHE 0.017 0.001 PHE E 67 TRP 0.002 0.001 TRP N1580 HIS 0.007 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.20 (14574) covalent geometry : angle 0.69208 / 0.40 (20910) hydrogen bonds : bond 0.06177 / 4.18 ( 743) hydrogen bonds : angle 4.15097 / 2.95 ( 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 271 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 249 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8641 (pp20) cc_final: 0.8426 (tm-30) REVERT: A 106 ASP cc_start: 0.9016 (m-30) cc_final: 0.8573 (m-30) REVERT: B 53 GLU cc_start: 0.8405 (pm20) cc_final: 0.8097 (pm20) REVERT: B 74 GLU cc_start: 0.9326 (mm-30) cc_final: 0.9125 (mm-30) REVERT: B 84 MET cc_start: 0.9265 (mmt) cc_final: 0.8732 (mmt) REVERT: B 85 ASP cc_start: 0.9159 (m-30) cc_final: 0.8760 (m-30) REVERT: B 88 TYR cc_start: 0.9204 (m-80) cc_final: 0.8955 (m-80) REVERT: C 56 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8702 (mm-30) REVERT: C 64 GLU cc_start: 0.9214 (tp30) cc_final: 0.8753 (tp30) REVERT: D 71 GLU cc_start: 0.9419 (mm-30) cc_final: 0.9100 (tp30) REVERT: E 80 THR cc_start: 0.9613 (m) cc_final: 0.9384 (t) REVERT: E 125 GLN cc_start: 0.9252 (mt0) cc_final: 0.9035 (mt0) REVERT: F 85 ASP cc_start: 0.9406 (m-30) cc_final: 0.9168 (m-30) REVERT: G 64 GLU cc_start: 0.9490 (tt0) cc_final: 0.8984 (tm-30) REVERT: G 72 ASP cc_start: 0.9303 (m-30) cc_final: 0.9048 (m-30) REVERT: G 92 GLU cc_start: 0.8759 (tt0) cc_final: 0.7989 (tt0) REVERT: O 40 GLN cc_start: 0.8186 (mm110) cc_final: 0.7839 (mm110) REVERT: O 54 ARG cc_start: 0.8832 (tpp80) cc_final: 0.8592 (tpp80) REVERT: O 62 GLN cc_start: 0.9150 (mm110) cc_final: 0.8725 (mm110) REVERT: O 69 LEU cc_start: 0.9584 (tp) cc_final: 0.9355 (pp) outliers start: 22 outliers final: 14 residues processed: 258 average time/residue: 0.1390 time to fit residues: 50.1018 Evaluate side-chains 234 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 220 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 63 GLU 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 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: 0.0170 chunk 45 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.7622 ------------------------------------------------------------------------------- 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 H 109 HIS ** 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 = 0.3327 r_free = 0.3327 target = 0.054766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.036177 restraints weight = 66583.465| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 3.41 r_work: 0.2508 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14574 Z= 0.152 Angle : 0.642 7.017 20910 Z= 0.377 Chirality : 0.043 0.249 2371 Planarity : 0.004 0.056 1646 Dihedral : 29.929 158.043 4264 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.56 % Allowed : 13.54 % Favored : 83.90 % 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: 0.16 (0.27), residues: 965 helix: 1.10 (0.22), residues: 555 sheet: -0.82 (0.77), residues: 29 loop : -1.30 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K1629 TYR 0.021 0.001 TYR H 83 PHE 0.012 0.001 PHE E 67 TRP 0.004 0.001 TRP N1580 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (14574) covalent geometry : angle 0.64237 / 0.38 (20910) hydrogen bonds : bond 0.05272 / 3.62 ( 743) hydrogen bonds : angle 3.81012 / 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 269 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 248 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9413 (mt-10) cc_final: 0.9058 (mt-10) REVERT: A 79 LYS cc_start: 0.9122 (mtpp) cc_final: 0.8842 (mtpt) REVERT: A 105 GLU cc_start: 0.8684 (pp20) cc_final: 0.8370 (tm-30) REVERT: A 106 ASP cc_start: 0.9088 (m-30) cc_final: 0.8584 (m-30) REVERT: B 63 GLU cc_start: 0.8759 (pm20) cc_final: 0.8500 (mp0) REVERT: B 84 MET cc_start: 0.9309 (mmt) cc_final: 0.8909 (mmt) REVERT: B 85 ASP cc_start: 0.9191 (m-30) cc_final: 0.8805 (m-30) REVERT: C 56 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8714 (mm-30) REVERT: C 64 GLU cc_start: 0.9229 (tp30) cc_final: 0.8766 (tp30) REVERT: D 71 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9115 (tp30) REVERT: E 105 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8611 (tm-30) REVERT: E 125 GLN cc_start: 0.9280 (mt0) cc_final: 0.9009 (mt0) REVERT: F 52 GLU cc_start: 0.8840 (mp0) cc_final: 0.8584 (pm20) REVERT: F 85 ASP cc_start: 0.9421 (m-30) cc_final: 0.9202 (m-30) REVERT: G 72 ASP cc_start: 0.9243 (m-30) cc_final: 0.8937 (m-30) REVERT: H 105 GLU cc_start: 0.8938 (pm20) cc_final: 0.8721 (pm20) REVERT: O 40 GLN cc_start: 0.8219 (mm110) cc_final: 0.7874 (mm110) REVERT: O 62 GLN cc_start: 0.9159 (mm110) cc_final: 0.8732 (mm110) outliers start: 21 outliers final: 14 residues processed: 256 average time/residue: 0.1299 time to fit residues: 47.3994 Evaluate side-chains 236 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 222 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 62 LEU 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 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: 3.9990 chunk 96 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 66 optimal weight: 0.0020 chunk 115 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 102 optimal weight: 0.0970 overall best weight: 2.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 93 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.053954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.035402 restraints weight = 65979.173| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 3.36 r_work: 0.2487 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14574 Z= 0.181 Angle : 0.656 7.672 20910 Z= 0.379 Chirality : 0.043 0.263 2371 Planarity : 0.004 0.060 1646 Dihedral : 30.050 159.911 4264 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.66 % Allowed : 13.78 % Favored : 82.56 % 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: 1.29 (0.22), residues: 555 sheet: -0.68 (0.95), residues: 24 loop : -1.31 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG D 31 TYR 0.034 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 TRP 0.003 0.001 TRP N1580 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.18 (14574) covalent geometry : angle 0.65635 / 0.38 (20910) hydrogen bonds : bond 0.05169 / 3.53 ( 743) hydrogen bonds : angle 3.72121 / 2.64 ( 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 262 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8345 (tm-30) REVERT: A 106 ASP cc_start: 0.9130 (m-30) cc_final: 0.8628 (m-30) REVERT: A 125 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.9015 (pm20) REVERT: B 63 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8290 (pm20) REVERT: B 84 MET cc_start: 0.9277 (mmt) cc_final: 0.8894 (mmt) REVERT: B 85 ASP cc_start: 0.9193 (m-30) cc_final: 0.8904 (m-30) REVERT: B 88 TYR cc_start: 0.9186 (m-80) cc_final: 0.8901 (m-80) REVERT: C 56 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8685 (mm-30) REVERT: D 71 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9205 (tp30) REVERT: E 105 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8661 (tm-30) REVERT: E 106 ASP cc_start: 0.9195 (m-30) cc_final: 0.8984 (m-30) REVERT: F 52 GLU cc_start: 0.8985 (mp0) cc_final: 0.8557 (pm20) REVERT: F 85 ASP cc_start: 0.9396 (m-30) cc_final: 0.9161 (m-30) REVERT: G 72 ASP cc_start: 0.9225 (m-30) cc_final: 0.8911 (m-30) REVERT: H 83 TYR cc_start: 0.8384 (m-80) cc_final: 0.8141 (m-80) REVERT: H 105 GLU cc_start: 0.8901 (pm20) cc_final: 0.8673 (pm20) REVERT: O 40 GLN cc_start: 0.8226 (mm110) cc_final: 0.7877 (mm110) outliers start: 30 outliers final: 21 residues processed: 241 average time/residue: 0.1326 time to fit residues: 45.0247 Evaluate side-chains 245 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 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 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: 0.2980 chunk 102 optimal weight: 0.0870 chunk 78 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 89 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 overall best weight: 3.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 H 47 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 = 0.3284 r_free = 0.3284 target = 0.053326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.034913 restraints weight = 66602.625| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 3.35 r_work: 0.2469 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14574 Z= 0.235 Angle : 0.687 7.594 20910 Z= 0.389 Chirality : 0.044 0.276 2371 Planarity : 0.004 0.058 1646 Dihedral : 30.184 160.558 4264 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.66 % Allowed : 16.34 % Favored : 80.00 % 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: 0.42 (0.27), residues: 965 helix: 1.38 (0.22), residues: 555 sheet: -0.61 (0.94), residues: 24 loop : -1.31 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 31 TYR 0.027 0.002 TYR B 88 PHE 0.010 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 0.00471 / 0.24 (14574) covalent geometry : angle 0.68677 / 0.39 (20910) hydrogen bonds : bond 0.05292 / 3.57 ( 743) hydrogen bonds : angle 3.71732 / 2.63 ( 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 258 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8405 (tm-30) REVERT: A 125 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8957 (pm20) REVERT: B 63 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8318 (pm20) REVERT: B 84 MET cc_start: 0.9274 (mmt) cc_final: 0.8915 (mmt) REVERT: B 85 ASP cc_start: 0.9215 (m-30) cc_final: 0.8933 (m-30) REVERT: B 88 TYR cc_start: 0.9243 (m-80) cc_final: 0.8909 (m-80) REVERT: C 56 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8818 (mm-30) REVERT: D 71 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9199 (tp30) REVERT: E 79 LYS cc_start: 0.8807 (ttpp) cc_final: 0.8437 (ttpp) REVERT: E 105 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8613 (tm-30) REVERT: F 52 GLU cc_start: 0.8994 (mp0) cc_final: 0.8542 (pm20) REVERT: F 85 ASP cc_start: 0.9428 (m-30) cc_final: 0.9192 (m-30) REVERT: G 72 ASP cc_start: 0.9216 (m-30) cc_final: 0.8901 (m-30) REVERT: H 34 LYS cc_start: 0.8946 (mmtm) cc_final: 0.8726 (mmtm) REVERT: H 105 GLU cc_start: 0.8954 (pm20) cc_final: 0.8647 (pm20) REVERT: O 40 GLN cc_start: 0.8260 (mm110) cc_final: 0.7897 (mm110) outliers start: 30 outliers final: 22 residues processed: 238 average time/residue: 0.1345 time to fit residues: 45.0350 Evaluate side-chains 240 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 D residue 45 LEU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 68 ASP 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: 3.9990 chunk 64 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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** 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 = 0.3279 r_free = 0.3279 target = 0.053099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.034602 restraints weight = 66216.106| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 3.32 r_work: 0.2457 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14574 Z= 0.228 Angle : 0.691 7.831 20910 Z= 0.392 Chirality : 0.044 0.285 2371 Planarity : 0.004 0.057 1646 Dihedral : 30.273 160.718 4264 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.39 % Allowed : 16.71 % Favored : 78.90 % 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: 0.43 (0.27), residues: 965 helix: 1.38 (0.22), residues: 555 sheet: -0.64 (0.93), residues: 24 loop : -1.29 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 79 TYR 0.025 0.002 TYR H 83 PHE 0.010 0.001 PHE E 67 TRP 0.004 0.001 TRP N1580 HIS 0.006 0.002 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.23 (14574) covalent geometry : angle 0.69123 / 0.39 (20910) hydrogen bonds : bond 0.05202 / 3.51 ( 743) hydrogen bonds : angle 3.71497 / 2.65 ( 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 265 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 229 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8490 (tm-30) REVERT: A 125 GLN cc_start: 0.9240 (OUTLIER) cc_final: 0.8923 (pm20) REVERT: B 53 GLU cc_start: 0.8243 (pm20) cc_final: 0.7731 (pm20) REVERT: B 63 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8317 (pm20) REVERT: B 84 MET cc_start: 0.9302 (mmt) cc_final: 0.9030 (mmt) REVERT: B 85 ASP cc_start: 0.9207 (m-30) cc_final: 0.8968 (m-30) REVERT: B 88 TYR cc_start: 0.9363 (m-80) cc_final: 0.9157 (m-80) REVERT: C 56 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8771 (mm-30) REVERT: D 71 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9195 (tp30) REVERT: E 79 LYS cc_start: 0.8856 (ttpp) cc_final: 0.8523 (ttpp) REVERT: E 105 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8711 (tm-30) REVERT: F 85 ASP cc_start: 0.9418 (m-30) cc_final: 0.9172 (m-30) REVERT: G 72 ASP cc_start: 0.9188 (m-30) cc_final: 0.8863 (m-30) REVERT: H 105 GLU cc_start: 0.8985 (pm20) cc_final: 0.8693 (pm20) REVERT: O 40 GLN cc_start: 0.8353 (mm110) cc_final: 0.8019 (mm110) outliers start: 36 outliers final: 24 residues processed: 242 average time/residue: 0.1290 time to fit residues: 43.7508 Evaluate side-chains 241 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 115 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** G 112 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.052985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.034361 restraints weight = 67213.189| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 3.35 r_work: 0.2448 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 14574 Z= 0.233 Angle : 0.710 9.352 20910 Z= 0.398 Chirality : 0.044 0.288 2371 Planarity : 0.004 0.057 1646 Dihedral : 30.303 161.062 4264 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.78 % Allowed : 18.05 % Favored : 78.17 % 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: 0.48 (0.27), residues: 965 helix: 1.40 (0.22), residues: 555 sheet: -0.62 (0.93), residues: 24 loop : -1.24 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 79 TYR 0.032 0.002 TYR D 83 PHE 0.010 0.001 PHE E 67 TRP 0.004 0.001 TRP N1580 HIS 0.007 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.23 (14574) covalent geometry : angle 0.70965 / 0.40 (20910) hydrogen bonds : bond 0.05193 / 3.50 ( 743) hydrogen bonds : angle 3.72039 / 2.64 ( 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: 31 poor density : 224 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8640 (mp0) REVERT: A 125 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.8917 (pm20) REVERT: B 63 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8272 (mp0) REVERT: B 84 MET cc_start: 0.9293 (mmt) cc_final: 0.9016 (mmt) REVERT: B 85 ASP cc_start: 0.9228 (m-30) cc_final: 0.9019 (m-30) REVERT: B 88 TYR cc_start: 0.9375 (m-80) cc_final: 0.9155 (m-80) REVERT: C 56 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8684 (mm-30) REVERT: C 90 ASP cc_start: 0.8505 (t0) cc_final: 0.8295 (t70) REVERT: D 71 GLU cc_start: 0.9428 (mm-30) cc_final: 0.9199 (tp30) REVERT: E 73 GLU cc_start: 0.9522 (tt0) cc_final: 0.9259 (tt0) REVERT: E 79 LYS cc_start: 0.8838 (ttpp) cc_final: 0.8578 (ttpp) REVERT: E 105 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8681 (tm-30) REVERT: F 85 ASP cc_start: 0.9424 (m-30) cc_final: 0.9183 (m-30) REVERT: G 72 ASP cc_start: 0.9172 (m-30) cc_final: 0.8854 (m-30) REVERT: H 105 GLU cc_start: 0.9042 (pm20) cc_final: 0.8758 (pm20) REVERT: O 40 GLN cc_start: 0.8358 (mm110) cc_final: 0.8026 (mm110) REVERT: O 62 GLN cc_start: 0.9241 (mm110) cc_final: 0.8870 (mm110) outliers start: 31 outliers final: 24 residues processed: 237 average time/residue: 0.1267 time to fit residues: 42.1281 Evaluate side-chains 242 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 46 ILE 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 106 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 111 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** 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** O 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.054120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.035546 restraints weight = 66390.585| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 3.32 r_work: 0.2486 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14574 Z= 0.154 Angle : 0.679 9.442 20910 Z= 0.386 Chirality : 0.043 0.285 2371 Planarity : 0.004 0.057 1646 Dihedral : 30.186 161.734 4264 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.56 % Allowed : 20.12 % 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: 0.53 (0.27), residues: 965 helix: 1.42 (0.22), residues: 554 sheet: -0.51 (0.99), residues: 24 loop : -1.19 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 79 TYR 0.036 0.002 TYR D 83 PHE 0.009 0.001 PHE E 67 TRP 0.003 0.001 TRP N1580 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (14574) covalent geometry : angle 0.67865 / 0.39 (20910) hydrogen bonds : bond 0.04669 / 3.20 ( 743) hydrogen bonds : angle 3.56010 / 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 257 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8559 (mp0) REVERT: A 125 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8872 (pm20) REVERT: B 63 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8229 (mp0) REVERT: B 85 ASP cc_start: 0.9216 (m-30) cc_final: 0.9007 (m-30) REVERT: C 56 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8721 (mm-30) REVERT: D 71 GLU cc_start: 0.9430 (mm-30) cc_final: 0.9160 (tp30) REVERT: E 73 GLU cc_start: 0.9507 (tt0) cc_final: 0.9270 (tt0) REVERT: E 79 LYS cc_start: 0.8809 (ttpp) cc_final: 0.8557 (ttpp) REVERT: E 105 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8653 (tm-30) REVERT: F 52 GLU cc_start: 0.8954 (mp0) cc_final: 0.8681 (pm20) REVERT: F 85 ASP cc_start: 0.9400 (m-30) cc_final: 0.9182 (m-30) REVERT: G 72 ASP cc_start: 0.9172 (m-30) cc_final: 0.8837 (m-30) REVERT: H 105 GLU cc_start: 0.9012 (pm20) cc_final: 0.8768 (pm20) REVERT: O 40 GLN cc_start: 0.8284 (mm110) cc_final: 0.7998 (mm110) REVERT: O 49 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7469 (mm-40) REVERT: O 62 GLN cc_start: 0.9233 (mm110) cc_final: 0.8857 (mm110) outliers start: 21 outliers final: 10 residues processed: 245 average time/residue: 0.1193 time to fit residues: 41.2729 Evaluate side-chains 239 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 225 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 114 VAL Chi-restraints excluded: chain O residue 4 PHE Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 31 GLN Chi-restraints excluded: chain O residue 49 GLN 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: 20.0000 chunk 32 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN ** 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.054391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.035971 restraints weight = 66514.403| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 3.31 r_work: 0.2508 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 14574 Z= 0.158 Angle : 0.687 10.211 20910 Z= 0.390 Chirality : 0.043 0.288 2371 Planarity : 0.004 0.059 1646 Dihedral : 30.138 163.450 4264 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.83 % Allowed : 21.59 % Favored : 76.59 % 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: 0.52 (0.27), residues: 965 helix: 1.39 (0.22), residues: 556 sheet: -0.57 (1.01), residues: 24 loop : -1.15 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 79 TYR 0.049 0.002 TYR D 83 PHE 0.008 0.001 PHE E 67 TRP 0.003 0.001 TRP N1580 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (14574) covalent geometry : angle 0.68729 / 0.39 (20910) hydrogen bonds : bond 0.04644 / 3.19 ( 743) hydrogen bonds : angle 3.53579 / 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 256 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 241 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.8828 (pm20) REVERT: B 63 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8214 (mp0) REVERT: C 56 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8735 (mm-30) REVERT: D 47 GLN cc_start: 0.9512 (mm-40) cc_final: 0.9293 (mm-40) REVERT: D 71 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9163 (tp30) REVERT: E 73 GLU cc_start: 0.9514 (tt0) cc_final: 0.9286 (tt0) REVERT: E 105 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8699 (tm-30) REVERT: F 52 GLU cc_start: 0.8950 (mp0) cc_final: 0.8666 (pm20) REVERT: F 85 ASP cc_start: 0.9359 (m-30) cc_final: 0.9148 (m-30) REVERT: G 72 ASP cc_start: 0.9160 (m-30) cc_final: 0.8847 (m-30) REVERT: H 120 LYS cc_start: 0.9562 (mtmt) cc_final: 0.9360 (mtmt) REVERT: O 40 GLN cc_start: 0.8217 (mm110) cc_final: 0.7908 (mm110) REVERT: O 62 GLN cc_start: 0.9196 (mm110) cc_final: 0.8812 (mm110) outliers start: 15 outliers final: 9 residues processed: 249 average time/residue: 0.1297 time to fit residues: 45.6222 Evaluate side-chains 241 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 230 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 114 VAL Chi-restraints excluded: chain O residue 4 PHE Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 31 GLN 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: 0.9980 chunk 97 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 66 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 99 optimal weight: 20.0000 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS E 108 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 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 = 0.3274 r_free = 0.3274 target = 0.052804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.034317 restraints weight = 67355.784| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 3.30 r_work: 0.2448 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 14574 Z= 0.268 Angle : 0.770 11.773 20910 Z= 0.422 Chirality : 0.045 0.308 2371 Planarity : 0.005 0.060 1646 Dihedral : 30.342 164.181 4264 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.95 % Allowed : 22.07 % Favored : 75.98 % 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: 0.52 (0.27), residues: 965 helix: 1.40 (0.22), residues: 555 sheet: -0.50 (0.94), residues: 24 loop : -1.17 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K1629 TYR 0.058 0.002 TYR D 83 PHE 0.011 0.001 PHE C 25 TRP 0.004 0.001 TRP N1580 HIS 0.007 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.27 (14574) covalent geometry : angle 0.76953 / 0.42 (20910) hydrogen bonds : bond 0.05478 / 3.66 ( 743) hydrogen bonds : angle 3.77982 / 2.68 ( 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 236 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 220 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8921 (mtpt) cc_final: 0.8602 (mtmt) REVERT: A 125 GLN cc_start: 0.9278 (OUTLIER) cc_final: 0.8920 (mp10) REVERT: B 63 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8345 (pm20) REVERT: B 85 ASP cc_start: 0.9218 (m-30) cc_final: 0.8886 (m-30) REVERT: C 56 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8681 (mm-30) REVERT: D 71 GLU cc_start: 0.9398 (mm-30) cc_final: 0.9179 (tp30) REVERT: E 73 GLU cc_start: 0.9498 (tt0) cc_final: 0.9284 (tt0) REVERT: E 105 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8706 (tm-30) REVERT: F 52 GLU cc_start: 0.8916 (mp0) cc_final: 0.8594 (pm20) REVERT: F 85 ASP cc_start: 0.9399 (m-30) cc_final: 0.9167 (m-30) REVERT: G 41 GLU cc_start: 0.9000 (mp0) cc_final: 0.8608 (mp0) REVERT: G 72 ASP cc_start: 0.9134 (m-30) cc_final: 0.8832 (m-30) REVERT: O 62 GLN cc_start: 0.9220 (mm110) cc_final: 0.8878 (mm110) outliers start: 16 outliers final: 12 residues processed: 226 average time/residue: 0.1271 time to fit residues: 40.3051 Evaluate side-chains 231 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 217 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 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 114 VAL Chi-restraints excluded: chain O residue 4 PHE Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 31 GLN 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: 0.9980 chunk 69 optimal weight: 0.8980 chunk 116 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3304 r_free = 0.3304 target = 0.053988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.035471 restraints weight = 67074.284| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 3.34 r_work: 0.2480 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2450 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= 0.162 Angle : 0.717 11.799 20910 Z= 0.401 Chirality : 0.044 0.305 2371 Planarity : 0.004 0.060 1646 Dihedral : 30.245 163.855 4264 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.83 % Allowed : 23.41 % Favored : 74.76 % 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: 0.52 (0.27), residues: 965 helix: 1.39 (0.22), residues: 554 sheet: -0.45 (0.96), residues: 24 loop : -1.17 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K1629 TYR 0.049 0.002 TYR B 88 PHE 0.008 0.001 PHE E 67 TRP 0.004 0.001 TRP N1580 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (14574) covalent geometry : angle 0.71706 / 0.40 (20910) hydrogen bonds : bond 0.04653 / 3.18 ( 743) hydrogen bonds : angle 3.59434 / 2.53 ( 1853) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3346.61 seconds wall clock time: 58 minutes 3.21 seconds (3483.21 seconds total)