Starting phenix.real_space_refine on Sat Aug 23 17:08:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqk_34028/08_2025/7yqk_34028.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqk_34028/08_2025/7yqk_34028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yqk_34028/08_2025/7yqk_34028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqk_34028/08_2025/7yqk_34028.map" model { file = "/net/cci-nas-00/data/ceres_data/7yqk_34028/08_2025/7yqk_34028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqk_34028/08_2025/7yqk_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 2.44, per 1000 atoms: 0.18 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: 1.03 Conformation dependent library (CDL) restraints added in 314.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.93 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: 2.28 Time building geometry restraints manager: 1.33 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=" CG1 ILE B 66 " pdb=" CD1 ILE B 66 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.27e+00 bond pdb=" CG LEU F 62 " pdb=" CD2 LEU F 62 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" C ILE A 119 " pdb=" N MET A 120 " ideal model delta sigma weight residual 1.325 1.310 0.015 1.25e-02 6.40e+03 1.52e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.19e+00 ... (remaining 14569 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 20186 1.61 - 3.22: 654 3.22 - 4.84: 52 4.84 - 6.45: 14 6.45 - 8.06: 4 Bond angle restraints: 20910 Sorted by residual: angle pdb=" N GLU B 63 " pdb=" CA GLU B 63 " pdb=" CB GLU B 63 " ideal model delta sigma weight residual 110.39 117.13 -6.74 1.75e+00 3.27e-01 1.48e+01 angle pdb=" C LEU B 62 " pdb=" N GLU B 63 " pdb=" CA GLU B 63 " ideal model delta sigma weight residual 121.18 114.67 6.51 1.98e+00 2.55e-01 1.08e+01 angle pdb=" C ILE A 124 " pdb=" N GLN A 125 " pdb=" CA GLN A 125 " ideal model delta sigma weight residual 121.58 115.37 6.21 1.95e+00 2.63e-01 1.02e+01 angle pdb=" CA GLU B 63 " pdb=" CB GLU B 63 " pdb=" CG GLU B 63 " ideal model delta sigma weight residual 114.10 119.71 -5.61 2.00e+00 2.50e-01 7.87e+00 angle pdb=" C TYR O 59 " pdb=" N ASN O 60 " pdb=" CA ASN O 60 " ideal model delta sigma weight residual 122.46 126.37 -3.91 1.41e+00 5.03e-01 7.69e+00 ... (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: 1538 0.032 - 0.064: 631 0.064 - 0.096: 141 0.096 - 0.128: 53 0.128 - 0.160: 8 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: 1.030 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.080 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 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 : 0.005 0.059 14574 Z= 0.226 Angle : 0.657 8.061 20910 Z= 0.394 Chirality : 0.038 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 aren 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 covalent geometry : bond 0.00488 (14574) covalent geometry : angle 0.65662 (20910) hydrogen bonds : bond 0.17655 ( 743) hydrogen bonds : angle 6.41787 ( 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 : 0.326 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: 0.8777 (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: 0.1101 time to fit residues: 39.7883 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 : 0.309 ------------------------------------------------------------------------------- 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: 5.9990 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 117 optimal weight: 30.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.055068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.036709 restraints weight = 65997.932| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.39 r_work: 0.2523 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14574 Z= 0.172 Angle : 0.601 6.211 20910 Z= 0.350 Chirality : 0.036 0.197 2371 Planarity : 0.004 0.056 1646 Dihedral : 29.507 156.386 4264 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.20 % Allowed : 10.61 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.27), residues: 965 helix: 1.05 (0.23), residues: 556 sheet: -0.68 (0.90), residues: 24 loop : -1.27 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 33 TYR 0.030 0.001 TYR H 83 PHE 0.012 0.001 PHE E 67 TRP 0.003 0.001 TRP N1580 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00378 (14574) covalent geometry : angle 0.60119 (20910) hydrogen bonds : bond 0.04729 ( 743) hydrogen bonds : angle 3.77352 ( 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 282 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 264 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 THR cc_start: 0.8597 (p) cc_final: 0.8378 (p) REVERT: A 94 GLU cc_start: 0.9258 (mm-30) cc_final: 0.9016 (mm-30) REVERT: A 105 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8395 (tm-30) REVERT: A 106 ASP cc_start: 0.8983 (m-30) cc_final: 0.8604 (m-30) REVERT: A 108 ASN cc_start: 0.9502 (OUTLIER) cc_final: 0.9169 (t0) REVERT: B 53 GLU cc_start: 0.8208 (pm20) cc_final: 0.7952 (pm20) REVERT: B 84 MET cc_start: 0.9332 (mmt) cc_final: 0.8946 (mmt) REVERT: B 85 ASP cc_start: 0.9235 (m-30) cc_final: 0.8950 (m-30) REVERT: B 88 TYR cc_start: 0.9246 (m-80) cc_final: 0.9017 (m-80) REVERT: C 56 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8655 (mm-30) REVERT: C 64 GLU cc_start: 0.9221 (tp30) cc_final: 0.8749 (tp30) REVERT: C 104 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8865 (mm-40) REVERT: D 71 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9217 (tp30) REVERT: E 80 THR cc_start: 0.9611 (m) cc_final: 0.9347 (t) REVERT: F 85 ASP cc_start: 0.9403 (m-30) cc_final: 0.9200 (m-30) REVERT: G 72 ASP cc_start: 0.9208 (m-30) cc_final: 0.8885 (m-30) REVERT: G 92 GLU cc_start: 0.8709 (tt0) cc_final: 0.8160 (tt0) REVERT: O 40 GLN cc_start: 0.8170 (mm110) cc_final: 0.7885 (mm110) outliers start: 18 outliers final: 12 residues processed: 270 average time/residue: 0.1131 time to fit residues: 42.3323 Evaluate side-chains 240 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 31 HIS 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 91 LYS 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 H residue 111 VAL Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 116 optimal weight: 0.0060 chunk 67 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 overall best weight: 1.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 84 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.054468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.035815 restraints weight = 67113.767| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 3.43 r_work: 0.2503 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14574 Z= 0.181 Angle : 0.596 7.351 20910 Z= 0.345 Chirality : 0.037 0.201 2371 Planarity : 0.004 0.059 1646 Dihedral : 29.560 157.648 4264 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.78 % Allowed : 13.41 % Favored : 82.80 % 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 aren not related in a simple way. whole: 0.51 (0.27), residues: 965 helix: 1.41 (0.23), residues: 556 sheet: -0.56 (0.96), residues: 24 loop : -1.22 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K1627 TYR 0.023 0.001 TYR D 83 PHE 0.011 0.001 PHE C 25 TRP 0.003 0.000 TRP N1580 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00401 (14574) covalent geometry : angle 0.59613 (20910) hydrogen bonds : bond 0.04378 ( 743) hydrogen bonds : angle 3.51918 ( 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 280 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 249 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8773 (mm-30) REVERT: A 105 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8375 (tm-30) REVERT: A 106 ASP cc_start: 0.9052 (m-30) cc_final: 0.8654 (m-30) REVERT: A 108 ASN cc_start: 0.9488 (OUTLIER) cc_final: 0.9256 (t0) REVERT: A 125 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.8938 (pm20) REVERT: B 63 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8355 (mp0) REVERT: B 85 ASP cc_start: 0.9228 (m-30) cc_final: 0.9025 (m-30) REVERT: C 56 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8777 (mm-30) REVERT: C 104 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8958 (mm-40) REVERT: D 34 LYS cc_start: 0.8771 (mmtm) cc_final: 0.8538 (mmtt) REVERT: D 47 GLN cc_start: 0.9571 (mm-40) cc_final: 0.9353 (mm-40) REVERT: D 71 GLU cc_start: 0.9429 (mm-30) cc_final: 0.9143 (tp30) REVERT: E 79 LYS cc_start: 0.8794 (ttpp) cc_final: 0.8443 (ttpp) REVERT: F 52 GLU cc_start: 0.9047 (mp0) cc_final: 0.8622 (pm20) REVERT: F 85 ASP cc_start: 0.9391 (m-30) cc_final: 0.9190 (m-30) REVERT: G 72 ASP cc_start: 0.9189 (m-30) cc_final: 0.8908 (m-30) REVERT: H 83 TYR cc_start: 0.8615 (m-80) cc_final: 0.8345 (m-80) REVERT: O 40 GLN cc_start: 0.8185 (mm110) cc_final: 0.7940 (mm110) REVERT: K 1626 LYS cc_start: 0.7810 (tptt) cc_final: 0.7465 (tptt) outliers start: 31 outliers final: 16 residues processed: 259 average time/residue: 0.1164 time to fit residues: 41.9451 Evaluate side-chains 249 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 229 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 108 ASN 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 31 HIS Chi-restraints excluded: chain C residue 62 ILE 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 H residue 111 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 66 THR Chi-restraints excluded: chain O residue 71 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 29 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 115 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.053855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.035468 restraints weight = 66565.181| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 3.32 r_work: 0.2487 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14574 Z= 0.205 Angle : 0.597 6.389 20910 Z= 0.347 Chirality : 0.037 0.202 2371 Planarity : 0.004 0.058 1646 Dihedral : 29.675 157.638 4264 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.90 % Allowed : 15.98 % Favored : 80.12 % 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 aren not related in a simple way. whole: 0.65 (0.27), residues: 965 helix: 1.50 (0.23), residues: 563 sheet: -0.38 (0.98), residues: 24 loop : -1.17 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 31 TYR 0.033 0.002 TYR D 83 PHE 0.011 0.001 PHE C 25 TRP 0.003 0.001 TRP N1580 HIS 0.006 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00459 (14574) covalent geometry : angle 0.59708 (20910) hydrogen bonds : bond 0.04391 ( 743) hydrogen bonds : angle 3.46231 ( 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 281 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 249 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8467 (tm-30) REVERT: A 106 ASP cc_start: 0.9077 (m-30) cc_final: 0.8624 (m-30) REVERT: A 108 ASN cc_start: 0.9486 (OUTLIER) cc_final: 0.9274 (t0) REVERT: A 125 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.8820 (pm20) REVERT: B 26 ILE cc_start: 0.9663 (tp) cc_final: 0.9446 (tp) REVERT: B 63 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8420 (mp0) REVERT: B 85 ASP cc_start: 0.9282 (m-30) cc_final: 0.9049 (m-30) REVERT: C 84 GLN cc_start: 0.9486 (OUTLIER) cc_final: 0.8996 (tt0) REVERT: C 104 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8975 (mm-40) REVERT: D 34 LYS cc_start: 0.8890 (mmtm) cc_final: 0.8678 (mmtm) REVERT: D 71 GLU cc_start: 0.9444 (mm-30) cc_final: 0.9141 (tp30) REVERT: E 125 GLN cc_start: 0.9250 (mt0) cc_final: 0.9007 (mt0) REVERT: F 52 GLU cc_start: 0.9033 (mp0) cc_final: 0.8610 (pm20) REVERT: F 85 ASP cc_start: 0.9353 (m-30) cc_final: 0.9133 (m-30) REVERT: G 31 HIS cc_start: 0.9031 (OUTLIER) cc_final: 0.8579 (m-70) REVERT: G 72 ASP cc_start: 0.9170 (m-30) cc_final: 0.8752 (m-30) REVERT: G 73 ASN cc_start: 0.9201 (m-40) cc_final: 0.8888 (t0) outliers start: 32 outliers final: 17 residues processed: 260 average time/residue: 0.1131 time to fit residues: 41.1272 Evaluate side-chains 253 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 108 ASN 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 84 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 108 ASN 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 15 LEU Chi-restraints excluded: chain O residue 31 GLN 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: 10.0000 chunk 102 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** G 94 ASN ** 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 = 0.3251 r_free = 0.3251 target = 0.051926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.033300 restraints weight = 67984.913| |-----------------------------------------------------------------------------| r_work (start): 0.2604 rms_B_bonded: 3.30 r_work: 0.2413 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 14574 Z= 0.337 Angle : 0.688 8.022 20910 Z= 0.391 Chirality : 0.041 0.204 2371 Planarity : 0.004 0.055 1646 Dihedral : 30.045 153.999 4264 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.02 % Allowed : 16.59 % Favored : 79.39 % 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 aren not related in a simple way. whole: 0.55 (0.27), residues: 965 helix: 1.41 (0.22), residues: 563 sheet: -0.39 (0.97), residues: 24 loop : -1.20 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K1629 TYR 0.044 0.002 TYR D 83 PHE 0.012 0.001 PHE E 67 TRP 0.004 0.001 TRP N1580 HIS 0.007 0.002 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00759 (14574) covalent geometry : angle 0.68824 (20910) hydrogen bonds : bond 0.05477 ( 743) hydrogen bonds : angle 3.78472 ( 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 266 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9104 (m-30) cc_final: 0.8890 (m-30) REVERT: B 63 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8459 (mp0) REVERT: B 85 ASP cc_start: 0.9170 (m-30) cc_final: 0.8861 (m-30) REVERT: C 84 GLN cc_start: 0.9519 (OUTLIER) cc_final: 0.9241 (tt0) REVERT: D 71 GLU cc_start: 0.9444 (mm-30) cc_final: 0.9215 (tp30) REVERT: E 79 LYS cc_start: 0.8893 (ttpp) cc_final: 0.8660 (ttpp) REVERT: E 120 MET cc_start: 0.9206 (mpp) cc_final: 0.8998 (mtm) REVERT: F 85 ASP cc_start: 0.9409 (m-30) cc_final: 0.9172 (m-30) REVERT: G 41 GLU cc_start: 0.9025 (mp0) cc_final: 0.8799 (mp0) REVERT: G 72 ASP cc_start: 0.9128 (m-30) cc_final: 0.8816 (m-30) REVERT: H 83 TYR cc_start: 0.8783 (m-80) cc_final: 0.8550 (m-80) REVERT: O 40 GLN cc_start: 0.8462 (mm110) cc_final: 0.8258 (mm110) REVERT: O 62 GLN cc_start: 0.9230 (mm110) cc_final: 0.8894 (mm110) outliers start: 33 outliers final: 23 residues processed: 247 average time/residue: 0.1095 time to fit residues: 38.2040 Evaluate side-chains 245 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 84 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 84 GLN 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 31 HIS Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 4 PHE Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 31 GLN Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 99 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN E 108 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** 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 = 0.3284 r_free = 0.3284 target = 0.053155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.034697 restraints weight = 67497.663| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 3.33 r_work: 0.2453 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.2557 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= 0.213 Angle : 0.632 8.312 20910 Z= 0.364 Chirality : 0.037 0.181 2371 Planarity : 0.004 0.056 1646 Dihedral : 29.845 155.497 4264 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.54 % Allowed : 18.90 % Favored : 77.56 % 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 aren not related in a simple way. whole: 0.64 (0.27), residues: 965 helix: 1.49 (0.22), residues: 563 sheet: -0.42 (0.94), residues: 24 loop : -1.17 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K1629 TYR 0.048 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 TRP 0.003 0.001 TRP N1580 HIS 0.006 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00481 (14574) covalent geometry : angle 0.63195 (20910) hydrogen bonds : bond 0.04385 ( 743) hydrogen bonds : angle 3.54462 ( 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 277 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 248 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8831 (mm-30) REVERT: A 106 ASP cc_start: 0.9129 (m-30) cc_final: 0.8900 (m-30) REVERT: A 125 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.8835 (pm20) REVERT: B 63 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8445 (mp0) REVERT: B 85 ASP cc_start: 0.9160 (m-30) cc_final: 0.8891 (m-30) REVERT: C 84 GLN cc_start: 0.9506 (OUTLIER) cc_final: 0.9058 (tt0) REVERT: D 31 ARG cc_start: 0.7451 (mmm160) cc_final: 0.7174 (mmm160) REVERT: D 71 GLU cc_start: 0.9450 (mm-30) cc_final: 0.9215 (tp30) REVERT: E 120 MET cc_start: 0.9237 (mpp) cc_final: 0.8966 (mtm) REVERT: F 52 GLU cc_start: 0.8928 (mp0) cc_final: 0.8619 (pm20) REVERT: F 85 ASP cc_start: 0.9401 (m-30) cc_final: 0.9186 (m-30) REVERT: G 41 GLU cc_start: 0.8994 (mp0) cc_final: 0.8773 (mp0) REVERT: G 72 ASP cc_start: 0.9155 (m-30) cc_final: 0.8706 (m-30) REVERT: G 73 ASN cc_start: 0.9211 (m-40) cc_final: 0.8918 (t0) REVERT: H 51 ASP cc_start: 0.8958 (p0) cc_final: 0.8689 (p0) REVERT: O 6 LYS cc_start: 0.9441 (mmmt) cc_final: 0.9073 (mmmt) REVERT: O 40 GLN cc_start: 0.8394 (mm110) cc_final: 0.8185 (mm110) REVERT: O 62 GLN cc_start: 0.9236 (mm110) cc_final: 0.8953 (mm110) outliers start: 29 outliers final: 15 residues processed: 259 average time/residue: 0.1123 time to fit residues: 41.0625 Evaluate side-chains 249 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 84 MET Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 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 O residue 4 PHE Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 115 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN E 108 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN O 31 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.053702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.035273 restraints weight = 67091.406| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 3.32 r_work: 0.2467 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14574 Z= 0.194 Angle : 0.635 9.084 20910 Z= 0.364 Chirality : 0.037 0.226 2371 Planarity : 0.004 0.056 1646 Dihedral : 29.778 155.973 4264 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.17 % Allowed : 20.12 % Favored : 76.71 % 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 aren not related in a simple way. whole: 0.63 (0.27), residues: 965 helix: 1.48 (0.22), residues: 563 sheet: -0.31 (0.95), residues: 24 loop : -1.17 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K1629 TYR 0.054 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 TRP 0.003 0.001 TRP N1580 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00439 (14574) covalent geometry : angle 0.63475 (20910) hydrogen bonds : bond 0.04288 ( 743) hydrogen bonds : angle 3.49665 ( 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 270 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9140 (mm-30) cc_final: 0.8907 (mm-30) REVERT: A 106 ASP cc_start: 0.9113 (m-30) cc_final: 0.8860 (m-30) REVERT: A 125 GLN cc_start: 0.9288 (OUTLIER) cc_final: 0.8832 (pm20) REVERT: B 59 LYS cc_start: 0.9305 (ttmt) cc_final: 0.8779 (ttpp) REVERT: B 63 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8423 (mp0) REVERT: B 85 ASP cc_start: 0.9166 (m-30) cc_final: 0.8933 (m-30) REVERT: C 56 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8616 (mm-30) REVERT: C 84 GLN cc_start: 0.9531 (OUTLIER) cc_final: 0.9002 (tt0) REVERT: D 31 ARG cc_start: 0.7493 (mmm160) cc_final: 0.7180 (mmm160) REVERT: D 71 GLU cc_start: 0.9445 (mm-30) cc_final: 0.9212 (tp30) REVERT: E 79 LYS cc_start: 0.8931 (ttpp) cc_final: 0.8397 (ttpp) REVERT: E 120 MET cc_start: 0.9247 (mpp) cc_final: 0.8941 (mtm) REVERT: F 52 GLU cc_start: 0.8915 (mp0) cc_final: 0.8608 (pm20) REVERT: F 85 ASP cc_start: 0.9378 (m-30) cc_final: 0.9165 (m-30) REVERT: G 31 HIS cc_start: 0.9211 (OUTLIER) cc_final: 0.8899 (t-90) REVERT: G 41 GLU cc_start: 0.9002 (mp0) cc_final: 0.8778 (mp0) REVERT: G 72 ASP cc_start: 0.9135 (m-30) cc_final: 0.8681 (m-30) REVERT: G 73 ASN cc_start: 0.9183 (m-40) cc_final: 0.8906 (t0) REVERT: H 34 LYS cc_start: 0.9180 (mmtm) cc_final: 0.8957 (mmtm) REVERT: H 51 ASP cc_start: 0.8938 (p0) cc_final: 0.8670 (p0) REVERT: O 6 LYS cc_start: 0.9496 (mmmt) cc_final: 0.9103 (mmmt) REVERT: O 62 GLN cc_start: 0.9218 (mm110) cc_final: 0.8899 (mm110) outliers start: 26 outliers final: 15 residues processed: 253 average time/residue: 0.1167 time to fit residues: 41.3839 Evaluate side-chains 251 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 231 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 31 HIS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 108 ASN 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 O residue 4 PHE Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain K residue 1619 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 106 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 111 optimal weight: 30.0000 chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN O 40 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 = 0.3299 r_free = 0.3299 target = 0.053926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.035413 restraints weight = 67281.421| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 3.36 r_work: 0.2489 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14574 Z= 0.184 Angle : 0.643 8.807 20910 Z= 0.367 Chirality : 0.037 0.260 2371 Planarity : 0.004 0.056 1646 Dihedral : 29.699 156.360 4264 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.17 % Allowed : 20.61 % Favored : 76.22 % 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 aren not related in a simple way. whole: 0.59 (0.27), residues: 965 helix: 1.44 (0.22), residues: 563 sheet: -0.07 (1.13), residues: 18 loop : -1.18 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K1629 TYR 0.056 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 covalent geometry : bond 0.00416 (14574) covalent geometry : angle 0.64271 (20910) hydrogen bonds : bond 0.04213 ( 743) hydrogen bonds : angle 3.48692 ( 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 277 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 251 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8933 (mm-30) REVERT: A 106 ASP cc_start: 0.9135 (m-30) cc_final: 0.8889 (m-30) REVERT: A 125 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.8827 (pm20) REVERT: B 59 LYS cc_start: 0.9277 (ttmt) cc_final: 0.8752 (ttpp) REVERT: B 63 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8411 (mp0) REVERT: B 85 ASP cc_start: 0.9141 (m-30) cc_final: 0.8935 (m-30) REVERT: C 84 GLN cc_start: 0.9514 (OUTLIER) cc_final: 0.8988 (tt0) REVERT: D 31 ARG cc_start: 0.7594 (mmm160) cc_final: 0.7310 (mmm160) REVERT: D 71 GLU cc_start: 0.9438 (mm-30) cc_final: 0.9211 (tp30) REVERT: E 120 MET cc_start: 0.9265 (mpp) cc_final: 0.8896 (mtm) REVERT: F 52 GLU cc_start: 0.8915 (mp0) cc_final: 0.8538 (pm20) REVERT: G 31 HIS cc_start: 0.9225 (OUTLIER) cc_final: 0.8956 (t-90) REVERT: G 41 GLU cc_start: 0.9012 (mp0) cc_final: 0.8777 (mp0) REVERT: G 72 ASP cc_start: 0.9167 (m-30) cc_final: 0.8726 (m-30) REVERT: G 73 ASN cc_start: 0.9147 (m-40) cc_final: 0.8909 (t0) REVERT: O 6 LYS cc_start: 0.9553 (mmmt) cc_final: 0.9185 (mmmt) REVERT: O 62 GLN cc_start: 0.9193 (mm110) cc_final: 0.8902 (mm110) outliers start: 26 outliers final: 16 residues processed: 262 average time/residue: 0.1112 time to fit residues: 40.8843 Evaluate side-chains 257 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 237 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 84 GLN Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 108 ASN 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 66 THR Chi-restraints excluded: chain K residue 1619 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 110 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.054896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.036446 restraints weight = 67679.284| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.39 r_work: 0.2522 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14574 Z= 0.162 Angle : 0.652 9.403 20910 Z= 0.369 Chirality : 0.037 0.226 2371 Planarity : 0.004 0.057 1646 Dihedral : 29.589 157.073 4264 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.29 % Allowed : 21.10 % Favored : 75.61 % 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 aren not related in a simple way. whole: 0.58 (0.27), residues: 965 helix: 1.45 (0.22), residues: 561 sheet: -0.88 (0.94), residues: 29 loop : -1.17 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K1629 TYR 0.039 0.002 TYR B 88 PHE 0.007 0.001 PHE E 67 TRP 0.002 0.000 TRP N1580 HIS 0.008 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00363 (14574) covalent geometry : angle 0.65169 (20910) hydrogen bonds : bond 0.04119 ( 743) hydrogen bonds : angle 3.48624 ( 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 281 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 254 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9132 (m-30) cc_final: 0.8926 (m-30) REVERT: B 59 LYS cc_start: 0.9273 (ttmt) cc_final: 0.8729 (ttpp) REVERT: B 63 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8322 (mp0) REVERT: C 84 GLN cc_start: 0.9511 (OUTLIER) cc_final: 0.8980 (tt0) REVERT: D 31 ARG cc_start: 0.7830 (mmm160) cc_final: 0.7573 (mmm160) REVERT: D 34 LYS cc_start: 0.9030 (mmtm) cc_final: 0.8697 (mmtm) REVERT: D 71 GLU cc_start: 0.9447 (mm-30) cc_final: 0.9199 (tp30) REVERT: E 79 LYS cc_start: 0.8920 (ttpp) cc_final: 0.8488 (ttpp) REVERT: F 44 LYS cc_start: 0.9306 (ttmt) cc_final: 0.8944 (ttmt) REVERT: F 52 GLU cc_start: 0.8868 (mp0) cc_final: 0.8566 (pm20) REVERT: G 31 HIS cc_start: 0.9186 (OUTLIER) cc_final: 0.8846 (t-90) REVERT: G 41 GLU cc_start: 0.9038 (mp0) cc_final: 0.8800 (mp0) REVERT: G 72 ASP cc_start: 0.9133 (m-30) cc_final: 0.8675 (m-30) REVERT: G 91 GLU cc_start: 0.9362 (pm20) cc_final: 0.8905 (pm20) REVERT: H 105 GLU cc_start: 0.8907 (pm20) cc_final: 0.8668 (pm20) REVERT: O 6 LYS cc_start: 0.9567 (mmmt) cc_final: 0.9195 (mmmt) outliers start: 27 outliers final: 18 residues processed: 263 average time/residue: 0.1132 time to fit residues: 42.1886 Evaluate side-chains 261 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 240 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE 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 84 GLN Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 108 ASN 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 79 ILE 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 66 THR Chi-restraints excluded: chain K residue 1619 LEU Chi-restraints excluded: chain N residue 1587 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 99 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS E 108 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** 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 = 0.3305 r_free = 0.3305 target = 0.054144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.035625 restraints weight = 67872.375| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 3.39 r_work: 0.2502 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 14574 Z= 0.200 Angle : 0.687 9.621 20910 Z= 0.388 Chirality : 0.038 0.201 2371 Planarity : 0.004 0.056 1646 Dihedral : 29.695 156.819 4264 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.68 % Allowed : 22.20 % Favored : 75.12 % 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 aren not related in a simple way. whole: 0.60 (0.27), residues: 965 helix: 1.45 (0.22), residues: 561 sheet: -0.79 (0.94), residues: 29 loop : -1.12 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K1629 TYR 0.040 0.002 TYR B 88 PHE 0.009 0.001 PHE E 67 TRP 0.003 0.001 TRP N1580 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00457 (14574) covalent geometry : angle 0.68671 (20910) hydrogen bonds : bond 0.04290 ( 743) hydrogen bonds : angle 3.60529 ( 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 261 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9096 (m-30) cc_final: 0.8796 (m-30) REVERT: B 59 LYS cc_start: 0.9274 (ttmt) cc_final: 0.8730 (ttpp) REVERT: B 63 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8338 (mp0) REVERT: C 84 GLN cc_start: 0.9529 (OUTLIER) cc_final: 0.9003 (tt0) REVERT: D 31 ARG cc_start: 0.7928 (mmm160) cc_final: 0.7713 (mmm160) REVERT: D 34 LYS cc_start: 0.9111 (mmtm) cc_final: 0.8785 (mmtm) REVERT: D 71 GLU cc_start: 0.9439 (mm-30) cc_final: 0.9179 (tp30) REVERT: F 44 LYS cc_start: 0.9316 (ttmt) cc_final: 0.8962 (ttmt) REVERT: F 52 GLU cc_start: 0.8854 (mp0) cc_final: 0.8537 (pm20) REVERT: G 41 GLU cc_start: 0.9048 (mp0) cc_final: 0.8819 (mp0) REVERT: G 72 ASP cc_start: 0.9092 (m-30) cc_final: 0.8847 (m-30) REVERT: H 83 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.7411 (t80) REVERT: H 93 GLU cc_start: 0.9062 (pm20) cc_final: 0.8853 (pm20) REVERT: H 105 GLU cc_start: 0.8733 (pm20) cc_final: 0.8228 (pm20) REVERT: O 6 LYS cc_start: 0.9552 (mmmt) cc_final: 0.9222 (mmmm) REVERT: O 62 GLN cc_start: 0.9202 (mm110) cc_final: 0.8923 (mm110) outliers start: 22 outliers final: 18 residues processed: 246 average time/residue: 0.1213 time to fit residues: 42.2155 Evaluate side-chains 249 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE 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 84 GLN Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 93 GLN 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 79 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain O residue 4 PHE Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain K residue 1619 LEU Chi-restraints excluded: chain N residue 1587 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 78 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 94 ASN ** 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 = 0.3325 r_free = 0.3325 target = 0.054943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.036220 restraints weight = 66878.186| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 3.36 r_work: 0.2525 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14574 Z= 0.173 Angle : 0.673 9.309 20910 Z= 0.379 Chirality : 0.037 0.207 2371 Planarity : 0.004 0.056 1646 Dihedral : 29.616 157.182 4264 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.68 % Allowed : 22.07 % Favored : 75.24 % 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 aren not related in a simple way. whole: 0.57 (0.27), residues: 965 helix: 1.38 (0.22), residues: 561 sheet: -0.78 (0.95), residues: 29 loop : -1.04 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K1629 TYR 0.033 0.002 TYR D 83 PHE 0.009 0.001 PHE E 67 TRP 0.004 0.001 TRP N1580 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00395 (14574) covalent geometry : angle 0.67252 (20910) hydrogen bonds : bond 0.04181 ( 743) hydrogen bonds : angle 3.57587 ( 1853) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2847.46 seconds wall clock time: 49 minutes 20.81 seconds (2960.81 seconds total)