Starting phenix.real_space_refine on Mon Dec 30 16:36:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqk_34028/12_2024/7yqk_34028.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqk_34028/12_2024/7yqk_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_34028/12_2024/7yqk_34028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqk_34028/12_2024/7yqk_34028.map" model { file = "/net/cci-nas-00/data/ceres_data/7yqk_34028/12_2024/7yqk_34028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqk_34028/12_2024/7yqk_34028.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 8.22, per 1000 atoms: 0.60 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: 3.18 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 6.74 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: 5.87 Time building geometry restraints manager: 3.74 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: 1.620 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: 0.530 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 37.720 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 43.230 ------------------------------------------------------------------------------- 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= 0.276 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (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 TRP 0.001 0.000 TRP N1495 HIS 0.007 0.001 HIS G 31 PHE 0.023 0.002 PHE C 25 TYR 0.032 0.002 TYR F 88 ARG 0.006 0.001 ARG D 79 *********************** 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 : 1.132 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: 0.2963 time to fit residues: 105.4578 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 : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1450 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= 0.226 Angle : 0.606 6.666 20910 Z= 0.353 Chirality : 0.037 0.194 2371 Planarity : 0.004 0.055 1646 Dihedral : 29.541 156.125 4264 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.20 % Allowed : 10.73 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.27), residues: 965 helix: 1.06 (0.23), residues: 556 sheet: -0.68 (0.90), residues: 24 loop : -1.28 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N1580 HIS 0.006 0.001 HIS B 75 PHE 0.012 0.001 PHE E 67 TYR 0.031 0.002 TYR H 83 ARG 0.010 0.001 ARG H 92 *********************** 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 279 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 261 time to evaluate : 1.158 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 94 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8773 (mm-30) REVERT: A 105 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7751 (tm-30) REVERT: A 106 ASP cc_start: 0.8628 (m-30) cc_final: 0.8096 (m-30) REVERT: A 108 ASN cc_start: 0.9382 (OUTLIER) cc_final: 0.9024 (t0) REVERT: B 53 GLU cc_start: 0.7956 (pm20) cc_final: 0.7734 (pm20) REVERT: B 84 MET cc_start: 0.8875 (mmt) cc_final: 0.8498 (mmt) REVERT: B 85 ASP cc_start: 0.8889 (m-30) cc_final: 0.8526 (m-30) REVERT: B 88 TYR cc_start: 0.9018 (m-80) cc_final: 0.8775 (m-80) REVERT: C 56 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8279 (mm-30) REVERT: C 64 GLU cc_start: 0.8865 (tp30) cc_final: 0.8409 (tp30) REVERT: C 104 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8659 (mm-40) REVERT: D 71 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8710 (tp30) REVERT: E 80 THR cc_start: 0.9429 (m) cc_final: 0.9166 (t) REVERT: F 31 LYS cc_start: 0.8800 (tttm) cc_final: 0.8593 (ttpp) REVERT: F 85 ASP cc_start: 0.9241 (m-30) cc_final: 0.8992 (m-30) REVERT: G 41 GLU cc_start: 0.8591 (mp0) cc_final: 0.8310 (mp0) REVERT: G 72 ASP cc_start: 0.8945 (m-30) cc_final: 0.8603 (m-30) REVERT: G 92 GLU cc_start: 0.8323 (tt0) cc_final: 0.7571 (tt0) REVERT: O 40 GLN cc_start: 0.7991 (mm110) cc_final: 0.7746 (mm110) outliers start: 18 outliers final: 12 residues processed: 267 average time/residue: 0.3197 time to fit residues: 118.0310 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 : 1.177 ------------------------------------------------------------------------------- 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 61 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 30 optimal weight: 0.1980 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 31 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 14574 Z= 0.309 Angle : 0.626 6.781 20910 Z= 0.361 Chirality : 0.038 0.174 2371 Planarity : 0.004 0.058 1646 Dihedral : 29.704 156.143 4264 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.78 % Allowed : 14.39 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.27), residues: 965 helix: 1.41 (0.22), residues: 558 sheet: -0.60 (0.97), residues: 24 loop : -1.23 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N1580 HIS 0.006 0.001 HIS G 31 PHE 0.012 0.001 PHE C 25 TYR 0.025 0.002 TYR D 83 ARG 0.009 0.000 ARG K1629 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1930 Ramachandran restraints generated. 965 Oldfield, 0 Emsley, 965 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7817 (tm-30) REVERT: A 106 ASP cc_start: 0.8750 (m-30) cc_final: 0.8185 (m-30) REVERT: A 108 ASN cc_start: 0.9364 (OUTLIER) cc_final: 0.9130 (t0) REVERT: A 125 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8737 (pm20) REVERT: B 63 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: B 85 ASP cc_start: 0.8885 (m-30) cc_final: 0.8658 (m-30) REVERT: C 56 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8378 (mm-30) REVERT: C 104 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8849 (mm-40) REVERT: D 47 GLN cc_start: 0.9390 (mm-40) cc_final: 0.9120 (mm-40) REVERT: D 71 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8723 (tp30) REVERT: D 89 ILE cc_start: 0.8867 (mt) cc_final: 0.8662 (mt) REVERT: E 79 LYS cc_start: 0.8738 (ttpp) cc_final: 0.8512 (ttpp) REVERT: F 31 LYS cc_start: 0.8914 (tttm) cc_final: 0.8649 (ttpp) REVERT: F 52 GLU cc_start: 0.8700 (mp0) cc_final: 0.8300 (pm20) REVERT: F 85 ASP cc_start: 0.9186 (m-30) cc_final: 0.8919 (m-30) REVERT: F 88 TYR cc_start: 0.8744 (m-10) cc_final: 0.8528 (m-10) REVERT: G 31 HIS cc_start: 0.8935 (OUTLIER) cc_final: 0.8381 (m-70) REVERT: G 41 GLU cc_start: 0.8676 (mp0) cc_final: 0.8401 (mp0) REVERT: G 72 ASP cc_start: 0.8919 (m-30) cc_final: 0.8642 (m-30) REVERT: H 83 TYR cc_start: 0.8463 (m-80) cc_final: 0.8136 (m-80) REVERT: O 40 GLN cc_start: 0.8057 (mm110) cc_final: 0.7787 (mm110) REVERT: K 1626 LYS cc_start: 0.7934 (tptt) cc_final: 0.7566 (tptt) outliers start: 31 outliers final: 16 residues processed: 251 average time/residue: 0.3282 time to fit residues: 114.5346 Evaluate side-chains 243 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 1.975 ------------------------------------------------------------------------------- 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 D residue 80 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 31 HIS Chi-restraints excluded: chain G residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** G 94 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2165 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= 0.197 Angle : 0.589 7.015 20910 Z= 0.342 Chirality : 0.036 0.176 2371 Planarity : 0.004 0.060 1646 Dihedral : 29.552 157.162 4264 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.90 % Allowed : 15.85 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.28), residues: 965 helix: 1.58 (0.23), residues: 557 sheet: -0.61 (0.95), residues: 24 loop : -1.13 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N1580 HIS 0.006 0.001 HIS B 75 PHE 0.009 0.001 PHE C 25 TYR 0.030 0.001 TYR D 83 ARG 0.007 0.000 ARG D 31 *********************** 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 286 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 254 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8389 (mm-30) REVERT: A 105 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7821 (tm-30) REVERT: A 106 ASP cc_start: 0.8794 (m-30) cc_final: 0.8278 (m-30) REVERT: A 108 ASN cc_start: 0.9362 (OUTLIER) cc_final: 0.9135 (t0) REVERT: A 125 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8625 (pm20) REVERT: B 63 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8074 (mp0) REVERT: B 84 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8427 (mmp) REVERT: B 85 ASP cc_start: 0.8924 (m-30) cc_final: 0.8716 (m-30) REVERT: C 56 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8364 (mm-30) REVERT: C 64 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8404 (tm-30) REVERT: C 68 ASN cc_start: 0.9221 (m-40) cc_final: 0.8925 (m-40) REVERT: C 84 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8883 (tt0) REVERT: C 104 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8665 (mm-40) REVERT: D 71 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8700 (tp30) REVERT: D 101 LEU cc_start: 0.9457 (mt) cc_final: 0.9255 (mt) REVERT: E 79 LYS cc_start: 0.8708 (ttpp) cc_final: 0.8198 (ttpp) REVERT: F 52 GLU cc_start: 0.8628 (mp0) cc_final: 0.8261 (pm20) REVERT: F 85 ASP cc_start: 0.9181 (m-30) cc_final: 0.8951 (m-30) REVERT: F 88 TYR cc_start: 0.8830 (m-10) cc_final: 0.8617 (m-10) REVERT: G 31 HIS cc_start: 0.8782 (OUTLIER) cc_final: 0.8582 (t-90) REVERT: G 41 GLU cc_start: 0.8657 (mp0) cc_final: 0.8327 (mp0) REVERT: G 72 ASP cc_start: 0.8908 (m-30) cc_final: 0.8509 (m-30) REVERT: G 73 ASN cc_start: 0.9105 (m-40) cc_final: 0.8792 (t0) REVERT: H 83 TYR cc_start: 0.8464 (m-10) cc_final: 0.8238 (m-80) REVERT: O 40 GLN cc_start: 0.8019 (mm110) cc_final: 0.7772 (mm110) REVERT: O 62 GLN cc_start: 0.9033 (mm110) cc_final: 0.8685 (mm110) outliers start: 32 outliers final: 14 residues processed: 265 average time/residue: 0.3076 time to fit residues: 114.4312 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 : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 66 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14574 Z= 0.211 Angle : 0.599 9.027 20910 Z= 0.345 Chirality : 0.036 0.212 2371 Planarity : 0.004 0.059 1646 Dihedral : 29.576 157.972 4264 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.05 % Allowed : 17.20 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.28), residues: 965 helix: 1.64 (0.22), residues: 563 sheet: -0.43 (1.02), residues: 24 loop : -1.18 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N1580 HIS 0.006 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.039 0.001 TYR D 83 ARG 0.004 0.000 ARG D 31 *********************** 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 273 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8534 (mm-30) REVERT: A 105 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: A 106 ASP cc_start: 0.8812 (m-30) cc_final: 0.8289 (m-30) REVERT: A 125 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8641 (pm20) REVERT: B 63 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: B 85 ASP cc_start: 0.8952 (m-30) cc_final: 0.8749 (m-30) REVERT: C 61 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8306 (mm-30) REVERT: C 64 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8365 (tm-30) REVERT: C 68 ASN cc_start: 0.9195 (m-40) cc_final: 0.8815 (m-40) REVERT: C 84 GLN cc_start: 0.9355 (OUTLIER) cc_final: 0.8877 (tt0) REVERT: C 104 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8692 (mm-40) REVERT: D 47 GLN cc_start: 0.9389 (mm-40) cc_final: 0.9099 (mm-40) REVERT: D 71 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8701 (tp30) REVERT: D 101 LEU cc_start: 0.9464 (mt) cc_final: 0.9247 (mt) REVERT: F 85 ASP cc_start: 0.9172 (m-30) cc_final: 0.8930 (m-30) REVERT: G 31 HIS cc_start: 0.8794 (OUTLIER) cc_final: 0.8208 (m-70) REVERT: G 41 GLU cc_start: 0.8711 (mp0) cc_final: 0.8337 (mp0) REVERT: G 72 ASP cc_start: 0.8889 (m-30) cc_final: 0.8455 (m-30) REVERT: G 73 ASN cc_start: 0.9074 (m-40) cc_final: 0.8793 (t0) REVERT: O 40 GLN cc_start: 0.8025 (mm110) cc_final: 0.7801 (mm110) REVERT: O 62 GLN cc_start: 0.9061 (mm110) cc_final: 0.8720 (mm110) outliers start: 25 outliers final: 13 residues processed: 257 average time/residue: 0.3260 time to fit residues: 117.9481 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 : 1.186 ------------------------------------------------------------------------------- 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 B residue 84 MET 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 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 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 56 LEU Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 112 optimal weight: 40.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14574 Z= 0.228 Angle : 0.611 8.613 20910 Z= 0.351 Chirality : 0.037 0.209 2371 Planarity : 0.004 0.059 1646 Dihedral : 29.640 157.920 4264 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.29 % Allowed : 17.93 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.27), residues: 965 helix: 1.64 (0.22), residues: 563 sheet: -0.44 (0.96), residues: 24 loop : -1.16 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N1580 HIS 0.006 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.042 0.002 TYR D 83 ARG 0.004 0.000 ARG O 72 *********************** 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 276 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 249 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8560 (mm-30) REVERT: A 97 GLU cc_start: 0.8080 (pp20) cc_final: 0.7868 (pp20) REVERT: A 105 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: A 106 ASP cc_start: 0.8849 (m-30) cc_final: 0.8332 (m-30) REVERT: A 125 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8648 (pm20) REVERT: B 59 LYS cc_start: 0.9135 (ttmt) cc_final: 0.8485 (ttpp) REVERT: B 63 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: C 56 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8511 (mm-30) REVERT: C 64 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8438 (tm-30) REVERT: C 68 ASN cc_start: 0.9186 (m-40) cc_final: 0.8804 (m-40) REVERT: C 84 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.8915 (tt0) REVERT: C 104 GLN cc_start: 0.8870 (mm-40) cc_final: 0.8611 (mm-40) REVERT: D 47 GLN cc_start: 0.9378 (mm-40) cc_final: 0.9116 (mm-40) REVERT: D 71 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8654 (tp30) REVERT: D 101 LEU cc_start: 0.9464 (mt) cc_final: 0.9241 (mt) REVERT: F 52 GLU cc_start: 0.8557 (mp0) cc_final: 0.8272 (pm20) REVERT: F 85 ASP cc_start: 0.9195 (m-30) cc_final: 0.8939 (m-30) REVERT: F 88 TYR cc_start: 0.8783 (m-10) cc_final: 0.8553 (m-10) REVERT: G 31 HIS cc_start: 0.8809 (OUTLIER) cc_final: 0.8292 (m-70) REVERT: G 41 GLU cc_start: 0.8719 (mp0) cc_final: 0.8335 (mp0) REVERT: G 72 ASP cc_start: 0.8883 (m-30) cc_final: 0.8452 (m-30) REVERT: G 73 ASN cc_start: 0.9078 (m-40) cc_final: 0.8833 (t0) REVERT: H 83 TYR cc_start: 0.8410 (m-10) cc_final: 0.8106 (m-80) REVERT: O 40 GLN cc_start: 0.8082 (mm110) cc_final: 0.7869 (mm110) REVERT: O 62 GLN cc_start: 0.9065 (mm110) cc_final: 0.8740 (mm110) outliers start: 27 outliers final: 15 residues processed: 257 average time/residue: 0.3079 time to fit residues: 110.2031 Evaluate side-chains 252 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE 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 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 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 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 13 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 116 optimal weight: 0.0050 chunk 72 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 0.0970 chunk 69 optimal weight: 0.7980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14574 Z= 0.186 Angle : 0.611 7.958 20910 Z= 0.349 Chirality : 0.036 0.218 2371 Planarity : 0.004 0.059 1646 Dihedral : 29.522 158.980 4264 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.32 % Allowed : 18.66 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.27), residues: 965 helix: 1.60 (0.22), residues: 562 sheet: 0.14 (1.15), residues: 18 loop : -1.20 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP N1580 HIS 0.005 0.001 HIS B 75 PHE 0.007 0.001 PHE A 67 TYR 0.041 0.001 TYR B 88 ARG 0.007 0.000 ARG K1629 *********************** 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 281 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 262 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8623 (mtmt) cc_final: 0.7970 (mtmt) REVERT: A 94 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8538 (mm-30) REVERT: A 97 GLU cc_start: 0.8098 (pp20) cc_final: 0.7837 (pp20) REVERT: A 106 ASP cc_start: 0.8846 (m-30) cc_final: 0.8592 (m-30) REVERT: A 125 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8645 (pm20) REVERT: B 59 LYS cc_start: 0.9118 (ttmt) cc_final: 0.8464 (ttpp) REVERT: B 63 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: B 74 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8612 (mm-30) REVERT: B 85 ASP cc_start: 0.8896 (m-30) cc_final: 0.8599 (m-30) REVERT: C 61 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8319 (mm-30) REVERT: C 64 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8442 (tm-30) REVERT: C 68 ASN cc_start: 0.9176 (m-40) cc_final: 0.8768 (m-40) REVERT: C 84 GLN cc_start: 0.9358 (OUTLIER) cc_final: 0.8919 (tt0) REVERT: C 104 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8498 (mm-40) REVERT: D 71 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8664 (tp30) REVERT: D 101 LEU cc_start: 0.9465 (mt) cc_final: 0.9258 (mt) REVERT: F 52 GLU cc_start: 0.8550 (mp0) cc_final: 0.8314 (pm20) REVERT: F 85 ASP cc_start: 0.9174 (m-30) cc_final: 0.8960 (m-30) REVERT: F 88 TYR cc_start: 0.8767 (m-10) cc_final: 0.8528 (m-10) REVERT: G 72 ASP cc_start: 0.8900 (m-30) cc_final: 0.8459 (m-30) REVERT: G 75 LYS cc_start: 0.9406 (mmtp) cc_final: 0.9009 (mmmm) REVERT: H 34 LYS cc_start: 0.9041 (mmtm) cc_final: 0.8833 (mmtm) REVERT: H 83 TYR cc_start: 0.8363 (m-10) cc_final: 0.8090 (m-80) REVERT: O 62 GLN cc_start: 0.9041 (mm110) cc_final: 0.8703 (mm110) outliers start: 19 outliers final: 9 residues processed: 268 average time/residue: 0.2919 time to fit residues: 109.4859 Evaluate side-chains 253 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 241 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 57 optimal weight: 0.0370 chunk 10 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 111 optimal weight: 0.1980 chunk 101 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 overall best weight: 2.4262 ------------------------------------------------------------------------------- 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 ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS G 73 ASN O 40 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14574 Z= 0.291 Angle : 0.657 9.839 20910 Z= 0.371 Chirality : 0.038 0.258 2371 Planarity : 0.004 0.059 1646 Dihedral : 29.814 157.594 4264 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.68 % Allowed : 20.12 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.27), residues: 965 helix: 1.60 (0.22), residues: 562 sheet: -0.02 (1.09), residues: 18 loop : -1.15 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N1580 HIS 0.008 0.001 HIS G 31 PHE 0.010 0.001 PHE E 67 TYR 0.046 0.002 TYR B 88 ARG 0.013 0.000 ARG K1629 *********************** 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 261 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8696 (mtmt) cc_final: 0.7960 (mtmt) REVERT: A 94 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8502 (mm-30) REVERT: A 106 ASP cc_start: 0.8847 (m-30) cc_final: 0.8388 (m-30) REVERT: A 125 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8684 (pm20) REVERT: B 59 LYS cc_start: 0.9152 (ttmt) cc_final: 0.8563 (ttpp) REVERT: B 63 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: B 74 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8639 (mm-30) REVERT: B 85 ASP cc_start: 0.8814 (m-30) cc_final: 0.8494 (m-30) REVERT: C 61 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8273 (mm-30) REVERT: C 64 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8619 (tm-30) REVERT: C 68 ASN cc_start: 0.9144 (m-40) cc_final: 0.8842 (m-40) REVERT: C 84 GLN cc_start: 0.9356 (OUTLIER) cc_final: 0.8904 (tt0) REVERT: D 47 GLN cc_start: 0.9304 (tp40) cc_final: 0.9048 (tp-100) REVERT: D 71 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8657 (tp30) REVERT: D 101 LEU cc_start: 0.9495 (mt) cc_final: 0.9291 (mt) REVERT: E 79 LYS cc_start: 0.8809 (ttpp) cc_final: 0.8304 (ttpp) REVERT: F 30 THR cc_start: 0.9074 (m) cc_final: 0.8800 (t) REVERT: F 52 GLU cc_start: 0.8555 (mp0) cc_final: 0.8302 (pm20) REVERT: F 85 ASP cc_start: 0.9153 (m-30) cc_final: 0.8901 (m-30) REVERT: G 41 GLU cc_start: 0.8776 (mp0) cc_final: 0.8563 (mp0) REVERT: G 72 ASP cc_start: 0.8779 (m-30) cc_final: 0.8514 (m-30) REVERT: H 34 LYS cc_start: 0.9092 (mmtm) cc_final: 0.8858 (mmtm) REVERT: H 83 TYR cc_start: 0.8552 (m-10) cc_final: 0.8285 (m-80) REVERT: O 18 GLU cc_start: 0.8966 (pm20) cc_final: 0.8760 (pm20) REVERT: O 62 GLN cc_start: 0.9067 (mm110) cc_final: 0.8789 (mm110) outliers start: 22 outliers final: 15 residues processed: 246 average time/residue: 0.3046 time to fit residues: 103.7932 Evaluate side-chains 245 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 94 ASN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 14574 Z= 0.320 Angle : 0.693 9.545 20910 Z= 0.388 Chirality : 0.039 0.178 2371 Planarity : 0.004 0.056 1646 Dihedral : 29.843 156.742 4264 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.68 % Allowed : 21.59 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.27), residues: 965 helix: 1.51 (0.22), residues: 560 sheet: -0.13 (1.06), residues: 18 loop : -1.14 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N1580 HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.048 0.002 TYR D 83 ARG 0.010 0.000 ARG K1629 *********************** 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 252 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8793 (m-30) cc_final: 0.8378 (m-30) REVERT: A 125 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8677 (pm20) REVERT: B 59 LYS cc_start: 0.9163 (ttmt) cc_final: 0.8589 (ttpp) REVERT: B 63 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8166 (mp0) REVERT: B 85 ASP cc_start: 0.8793 (m-30) cc_final: 0.8478 (m-30) REVERT: C 61 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8287 (mm-30) REVERT: C 64 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8614 (tm-30) REVERT: C 84 GLN cc_start: 0.9355 (OUTLIER) cc_final: 0.8867 (tt0) REVERT: D 34 LYS cc_start: 0.8930 (mppt) cc_final: 0.8725 (mppt) REVERT: D 47 GLN cc_start: 0.9322 (tp40) cc_final: 0.9080 (tp-100) REVERT: D 71 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8656 (tp30) REVERT: D 101 LEU cc_start: 0.9499 (mt) cc_final: 0.9298 (mt) REVERT: D 121 TYR cc_start: 0.9417 (t80) cc_final: 0.9160 (t80) REVERT: E 79 LYS cc_start: 0.8803 (ttpp) cc_final: 0.8404 (ttpp) REVERT: F 30 THR cc_start: 0.9061 (m) cc_final: 0.8835 (t) REVERT: F 52 GLU cc_start: 0.8524 (mp0) cc_final: 0.8263 (pm20) REVERT: F 85 ASP cc_start: 0.9167 (m-30) cc_final: 0.8906 (m-30) REVERT: G 41 GLU cc_start: 0.8776 (mp0) cc_final: 0.8552 (mp0) REVERT: G 72 ASP cc_start: 0.8764 (m-30) cc_final: 0.8518 (m-30) REVERT: H 34 LYS cc_start: 0.9140 (mmtm) cc_final: 0.8897 (mmtm) REVERT: H 83 TYR cc_start: 0.8536 (m-10) cc_final: 0.8146 (m-80) REVERT: H 105 GLU cc_start: 0.8485 (pm20) cc_final: 0.8282 (pm20) REVERT: O 18 GLU cc_start: 0.8925 (pm20) cc_final: 0.8718 (pm20) REVERT: O 62 GLN cc_start: 0.9088 (mm110) cc_final: 0.8813 (mm110) outliers start: 22 outliers final: 14 residues processed: 239 average time/residue: 0.2919 time to fit residues: 97.9156 Evaluate side-chains 237 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 220 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 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 40 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 9 THR Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 110 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 9 optimal weight: 0.0870 chunk 74 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- 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 76 GLN E 108 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 14574 Z= 0.374 Angle : 0.724 10.470 20910 Z= 0.405 Chirality : 0.041 0.191 2371 Planarity : 0.004 0.056 1646 Dihedral : 29.991 154.483 4264 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.44 % Allowed : 21.83 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.27), residues: 965 helix: 1.37 (0.22), residues: 561 sheet: -0.19 (1.04), residues: 18 loop : -1.16 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N1495 HIS 0.007 0.002 HIS B 75 PHE 0.011 0.001 PHE E 67 TYR 0.062 0.002 TYR D 83 ARG 0.013 0.001 ARG K1629 ********************** 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 245 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 225 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8767 (m-30) cc_final: 0.8402 (m-30) REVERT: A 125 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8670 (pm20) REVERT: B 59 LYS cc_start: 0.9179 (ttmt) cc_final: 0.8566 (ttpp) REVERT: B 63 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: B 85 ASP cc_start: 0.8770 (m-30) cc_final: 0.8435 (m-30) REVERT: C 56 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8423 (mt-10) REVERT: C 64 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8608 (tm-30) REVERT: C 84 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.8878 (tt0) REVERT: D 34 LYS cc_start: 0.8968 (mppt) cc_final: 0.8730 (mppt) REVERT: D 47 GLN cc_start: 0.9337 (tp40) cc_final: 0.9109 (tp-100) REVERT: D 71 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8661 (tp30) REVERT: E 73 GLU cc_start: 0.7852 (pt0) cc_final: 0.7318 (pt0) REVERT: F 25 ASN cc_start: 0.9191 (t0) cc_final: 0.8742 (t0) REVERT: F 85 ASP cc_start: 0.9183 (m-30) cc_final: 0.8912 (m-30) REVERT: G 41 GLU cc_start: 0.8727 (mp0) cc_final: 0.8511 (mp0) REVERT: G 72 ASP cc_start: 0.8770 (m-30) cc_final: 0.8535 (m-30) REVERT: H 34 LYS cc_start: 0.9205 (mmtm) cc_final: 0.8994 (mmtm) REVERT: H 105 GLU cc_start: 0.8301 (pm20) cc_final: 0.8057 (pm20) outliers start: 20 outliers final: 16 residues processed: 232 average time/residue: 0.2927 time to fit residues: 95.4333 Evaluate side-chains 236 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 217 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 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 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 N residue 1587 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** E 113 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 = 0.3299 r_free = 0.3299 target = 0.053935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.035314 restraints weight = 67183.859| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 3.36 r_work: 0.2491 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14574 Z= 0.228 Angle : 0.688 10.218 20910 Z= 0.384 Chirality : 0.038 0.199 2371 Planarity : 0.004 0.059 1646 Dihedral : 29.709 155.791 4264 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.32 % Allowed : 22.32 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.27), residues: 965 helix: 1.37 (0.22), residues: 561 sheet: -1.12 (0.87), residues: 29 loop : -1.12 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N1580 HIS 0.007 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.048 0.002 TYR D 83 ARG 0.012 0.000 ARG K1629 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2949.52 seconds wall clock time: 54 minutes 24.93 seconds (3264.93 seconds total)