Starting phenix.real_space_refine on Wed Mar 4 18:38:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sz7_55361/03_2026/9sz7_55361.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sz7_55361/03_2026/9sz7_55361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sz7_55361/03_2026/9sz7_55361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sz7_55361/03_2026/9sz7_55361.map" model { file = "/net/cci-nas-00/data/ceres_data/9sz7_55361/03_2026/9sz7_55361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sz7_55361/03_2026/9sz7_55361.cif" } resolution = 3.87 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= 0.012 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 205 5.49 5 S 29 5.16 5 C 9118 2.51 5 N 2656 2.21 5 O 3346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15354 Number of models: 1 Model: "" Number of chains: 16 Chain: "C" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1128 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "A" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1137 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain: "Y" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 981 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "Z" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 965 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "E" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1128 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "F" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1120 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "H" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1127 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "I" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1128 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "J" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1104 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain breaks: 1 Chain: "B" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1128 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "D" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1128 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "y" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 604 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "z" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 585 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "k" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 586 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "l" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 481 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "K" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 1 Time building chain proxies: 3.14, per 1000 atoms: 0.20 Number of scatterers: 15354 At special positions: 0 Unit cell: (101.813, 163.982, 178.398, 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 29 16.00 P 205 15.00 O 3346 8.00 N 2656 7.00 C 9118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 307.1 milliseconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2670 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 17 sheets defined 39.9% alpha, 14.4% beta 90 base pairs and 170 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'C' and resid 19 through 23 Processing helix chain 'C' and resid 44 through 57 Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 117 through 125 Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.663A pdb=" N SER A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.589A pdb=" N GLU A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 90 through 97 removed outlier: 3.627A pdb=" N SER A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'E' and resid 22 through 26 Processing helix chain 'E' and resid 47 through 58 removed outlier: 3.553A pdb=" N ASN E 57 " --> pdb=" O GLN E 53 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE E 58 " --> pdb=" O THR E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 75 removed outlier: 3.995A pdb=" N ARG E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 96 removed outlier: 3.764A pdb=" N ASP E 96 " --> pdb=" O ASN E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 126 Processing helix chain 'E' and resid 129 through 137 Processing helix chain 'F' and resid 47 through 56 removed outlier: 4.022A pdb=" N TYR F 51 " --> pdb=" O ASP F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 73 Processing helix chain 'F' and resid 90 through 98 removed outlier: 3.783A pdb=" N SER F 95 " --> pdb=" O ASN F 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA F 97 " --> pdb=" O LEU F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 124 removed outlier: 3.639A pdb=" N TYR F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU F 121 " --> pdb=" O LYS F 117 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN F 122 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR F 123 " --> pdb=" O GLN F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 135 removed outlier: 3.710A pdb=" N GLU F 135 " --> pdb=" O GLU F 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 23 removed outlier: 3.531A pdb=" N ARG H 23 " --> pdb=" O ALA H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 56 removed outlier: 4.283A pdb=" N SER H 50 " --> pdb=" O ALA H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 76 removed outlier: 3.551A pdb=" N ALA H 74 " --> pdb=" O ARG H 70 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASN H 75 " --> pdb=" O LEU H 71 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA H 76 " --> pdb=" O ILE H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 97 Processing helix chain 'H' and resid 117 through 126 Processing helix chain 'H' and resid 129 through 138 Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.550A pdb=" N SER I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE I 25 " --> pdb=" O LYS I 21 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE I 26 " --> pdb=" O LEU I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 56 Processing helix chain 'I' and resid 62 through 73 Processing helix chain 'I' and resid 81 through 86 removed outlier: 4.027A pdb=" N ASN I 85 " --> pdb=" O LEU I 81 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG I 86 " --> pdb=" O ASP I 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 81 through 86' Processing helix chain 'I' and resid 90 through 97 removed outlier: 3.687A pdb=" N SER I 95 " --> pdb=" O ASN I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 124 Processing helix chain 'I' and resid 130 through 137 Processing helix chain 'J' and resid 21 through 26 removed outlier: 3.770A pdb=" N PHE J 25 " --> pdb=" O LYS J 21 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE J 26 " --> pdb=" O LEU J 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 21 through 26' Processing helix chain 'J' and resid 46 through 56 removed outlier: 3.996A pdb=" N THR J 54 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN J 56 " --> pdb=" O PHE J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 74 removed outlier: 3.539A pdb=" N LEU J 71 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE J 72 " --> pdb=" O LEU J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 95 removed outlier: 3.881A pdb=" N SER J 95 " --> pdb=" O ASN J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 125 Processing helix chain 'J' and resid 129 through 137 removed outlier: 3.819A pdb=" N VAL J 133 " --> pdb=" O SER J 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.744A pdb=" N SER B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 removed outlier: 3.532A pdb=" N ASN B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 75 removed outlier: 3.813A pdb=" N ASN B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 98 Processing helix chain 'B' and resid 117 through 126 Processing helix chain 'B' and resid 129 through 136 Processing helix chain 'D' and resid 19 through 24 removed outlier: 3.743A pdb=" N SER D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 49 through 55 removed outlier: 3.586A pdb=" N THR D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 73 Processing helix chain 'D' and resid 90 through 95 removed outlier: 3.637A pdb=" N SER D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'K' and resid 19 through 23 Processing helix chain 'K' and resid 44 through 54 removed outlier: 3.730A pdb=" N THR K 54 " --> pdb=" O SER K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 73 Processing helix chain 'K' and resid 90 through 97 removed outlier: 3.554A pdb=" N SER K 95 " --> pdb=" O ASN K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 125 Processing helix chain 'K' and resid 129 through 136 removed outlier: 3.533A pdb=" N GLU K 135 " --> pdb=" O GLU K 131 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 5 through 9 Processing sheet with id=AA2, first strand: chain 'C' and resid 16 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 5 through 9 removed outlier: 3.625A pdb=" N CYS A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 6 through 9 removed outlier: 3.711A pdb=" N CYS E 39 " --> pdb=" O GLY E 35 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 76 through 79 removed outlier: 3.633A pdb=" N LEU F 40 " --> pdb=" O VAL F 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 7 through 9 removed outlier: 3.773A pdb=" N LEU H 40 " --> pdb=" O VAL H 114 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS H 39 " --> pdb=" O GLY H 35 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE H 30 " --> pdb=" O VAL H 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 6 through 7 Processing sheet with id=AA8, first strand: chain 'I' and resid 33 through 34 Processing sheet with id=AA9, first strand: chain 'J' and resid 6 through 9 Processing sheet with id=AB1, first strand: chain 'J' and resid 41 through 43 Processing sheet with id=AB2, first strand: chain 'B' and resid 6 through 8 removed outlier: 4.033A pdb=" N ILE B 103 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 16 through 17 Processing sheet with id=AB4, first strand: chain 'B' and resid 76 through 78 removed outlier: 3.644A pdb=" N CYS B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 6 through 8 removed outlier: 3.640A pdb=" N CYS D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 15 through 17 Processing sheet with id=AB7, first strand: chain 'K' and resid 6 through 9 removed outlier: 3.610A pdb=" N ILE K 30 " --> pdb=" O VAL K 79 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL K 79 " --> pdb=" O ILE K 30 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 15 through 17 420 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 205 hydrogen bonds 390 hydrogen bond angles 0 basepair planarities 90 basepair parallelities 170 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.36 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: 2846 1.33 - 1.45: 4688 1.45 - 1.57: 8066 1.57 - 1.69: 404 1.69 - 1.81: 48 Bond restraints: 16052 Sorted by residual: bond pdb=" C3' DG k -1 " pdb=" O3' DG k -1 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.74e+00 bond pdb=" C3' DA z 29 " pdb=" O3' DA z 29 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.25e+00 bond pdb=" CA SER H 95 " pdb=" C SER H 95 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.41e-02 5.03e+03 2.14e+00 bond pdb=" CA ASN J 14 " pdb=" C ASN J 14 " ideal model delta sigma weight residual 1.529 1.514 0.015 1.04e-02 9.25e+03 2.10e+00 bond pdb=" C3' DT y -16 " pdb=" O3' DT y -16 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.68e+00 ... (remaining 16047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 21427 1.72 - 3.44: 1020 3.44 - 5.16: 99 5.16 - 6.88: 20 6.88 - 8.59: 4 Bond angle restraints: 22570 Sorted by residual: angle pdb=" C LYS H 63 " pdb=" N ASP H 64 " pdb=" CA ASP H 64 " ideal model delta sigma weight residual 121.54 130.13 -8.59 1.91e+00 2.74e-01 2.02e+01 angle pdb=" C PRO B 59 " pdb=" N ASN B 60 " pdb=" CA ASN B 60 " ideal model delta sigma weight residual 121.54 129.75 -8.21 1.91e+00 2.74e-01 1.85e+01 angle pdb=" N ASN A 57 " pdb=" CA ASN A 57 " pdb=" C ASN A 57 " ideal model delta sigma weight residual 114.75 109.40 5.35 1.26e+00 6.30e-01 1.80e+01 angle pdb=" N ASN H 57 " pdb=" CA ASN H 57 " pdb=" C ASN H 57 " ideal model delta sigma weight residual 114.09 107.94 6.15 1.55e+00 4.16e-01 1.58e+01 angle pdb=" C SER D 29 " pdb=" N ILE D 30 " pdb=" CA ILE D 30 " ideal model delta sigma weight residual 121.97 129.00 -7.03 1.80e+00 3.09e-01 1.53e+01 ... (remaining 22565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.25: 7943 34.25 - 68.50: 1231 68.50 - 102.75: 34 102.75 - 137.00: 15 137.00 - 171.25: 18 Dihedral angle restraints: 9241 sinusoidal: 5188 harmonic: 4053 Sorted by residual: dihedral pdb=" CA SER D 28 " pdb=" C SER D 28 " pdb=" N SER D 29 " pdb=" CA SER D 29 " ideal model delta harmonic sigma weight residual 180.00 -150.89 -29.11 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA ASP E 27 " pdb=" C ASP E 27 " pdb=" N SER E 28 " pdb=" CA SER E 28 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA SER E 28 " pdb=" C SER E 28 " pdb=" N SER E 29 " pdb=" CA SER E 29 " ideal model delta harmonic sigma weight residual 180.00 152.92 27.08 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 9238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1616 0.034 - 0.068: 643 0.068 - 0.102: 213 0.102 - 0.135: 78 0.135 - 0.169: 12 Chirality restraints: 2562 Sorted by residual: chirality pdb=" CA VAL B 114 " pdb=" N VAL B 114 " pdb=" C VAL B 114 " pdb=" CB VAL B 114 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" P DA k -3 " pdb=" OP1 DA k -3 " pdb=" OP2 DA k -3 " pdb=" O5' DA k -3 " both_signs ideal model delta sigma weight residual True 2.35 -2.51 -0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" P DT z 42 " pdb=" OP1 DT z 42 " pdb=" OP2 DT z 42 " pdb=" O5' DT z 42 " both_signs ideal model delta sigma weight residual True 2.35 -2.51 -0.16 2.00e-01 2.50e+01 6.37e-01 ... (remaining 2559 not shown) Planarity restraints: 2195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG k 9 " -0.035 2.00e-02 2.50e+03 1.53e-02 7.01e+00 pdb=" N9 DG k 9 " 0.036 2.00e-02 2.50e+03 pdb=" C8 DG k 9 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG k 9 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG k 9 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG k 9 " -0.001 2.00e-02 2.50e+03 pdb=" O6 DG k 9 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DG k 9 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG k 9 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG k 9 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG k 9 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG k 9 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT z 31 " -0.030 2.00e-02 2.50e+03 1.34e-02 4.48e+00 pdb=" N1 DT z 31 " 0.024 2.00e-02 2.50e+03 pdb=" C2 DT z 31 " -0.000 2.00e-02 2.50e+03 pdb=" O2 DT z 31 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DT z 31 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT z 31 " -0.005 2.00e-02 2.50e+03 pdb=" O4 DT z 31 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DT z 31 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT z 31 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DT z 31 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA y -14 " 0.027 2.00e-02 2.50e+03 1.19e-02 3.87e+00 pdb=" N9 DA y -14 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA y -14 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DA y -14 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA y -14 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA y -14 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA y -14 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA y -14 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA y -14 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA y -14 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA y -14 " -0.001 2.00e-02 2.50e+03 ... (remaining 2192 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 37 2.57 - 3.15: 13261 3.15 - 3.74: 27877 3.74 - 4.32: 36030 4.32 - 4.90: 52860 Nonbonded interactions: 130065 Sorted by model distance: nonbonded pdb=" N2 DG k 9 " pdb=" O2 DC l 10 " model vdw 1.989 2.496 nonbonded pdb=" N7 DA y -27 " pdb=" O2 DT z 46 " model vdw 2.059 2.496 nonbonded pdb=" N2 DG Y 11 " pdb=" O2 DC Z 8 " model vdw 2.138 2.496 nonbonded pdb=" N1 DG k 9 " pdb=" N3 DC l 10 " model vdw 2.356 2.560 nonbonded pdb=" O5' DC Z 10 " pdb=" O4' DC Z 10 " model vdw 2.449 2.432 ... (remaining 130060 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 1 through 54 or resid 67 through 136)) selection = (chain 'B' and (resid 1 through 54 or resid 67 through 136)) selection = (chain 'C' and (resid 1 through 54 or resid 67 through 136)) selection = (chain 'D' and (resid 1 through 54 or resid 67 through 136)) selection = (chain 'E' and (resid 1 through 54 or resid 67 through 136)) selection = (chain 'F' and (resid 1 through 54 or resid 67 through 136)) selection = (chain 'H' and (resid 1 through 54 or resid 67 through 136)) selection = (chain 'I' and (resid 1 through 54 or resid 67 through 136)) selection = (chain 'J' and (resid 1 through 54 or resid 67 through 136)) selection = (chain 'K' and resid 1 through 136) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 11.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.590 Find NCS groups from input model: 0.200 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 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 0.060 16052 Z= 0.214 Angle : 0.782 8.595 22570 Z= 0.457 Chirality : 0.043 0.169 2562 Planarity : 0.004 0.049 2195 Dihedral : 26.741 171.249 6571 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 1.64 % Allowed : 17.90 % Favored : 80.46 % Rotamer: Outliers : 11.63 % Allowed : 14.50 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.21), residues: 1341 helix: -1.58 (0.21), residues: 480 sheet: -1.73 (0.29), residues: 310 loop : -3.26 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 70 TYR 0.016 0.001 TYR B 51 PHE 0.014 0.001 PHE J 109 TRP 0.014 0.002 TRP F 115 HIS 0.004 0.001 HIS J 111 Details of bonding type rmsd covalent geometry : bond 0.00455 (16052) covalent geometry : angle 0.78214 (22570) hydrogen bonds : bond 0.18004 ( 625) hydrogen bonds : angle 7.94673 ( 1539) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 286 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 109 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.8134 (m-80) REVERT: C 132 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8529 (p) REVERT: A 21 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7987 (mtmm) REVERT: E 31 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8655 (m) REVERT: F 89 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6946 (pt) REVERT: F 110 ASP cc_start: 0.6590 (p0) cc_final: 0.6150 (p0) REVERT: J 3 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7795 (tt) REVERT: J 39 CYS cc_start: 0.5048 (OUTLIER) cc_final: 0.4799 (t) REVERT: J 70 ARG cc_start: 0.5768 (OUTLIER) cc_final: 0.5541 (mtt180) REVERT: D 130 LEU cc_start: 0.8326 (tp) cc_final: 0.8088 (tp) outliers start: 146 outliers final: 53 residues processed: 386 average time/residue: 0.1268 time to fit residues: 70.8960 Evaluate side-chains 220 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 159 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 138 LYS Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 48 PHE Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain J residue 70 ARG Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain K residue 0 HIS Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN C 33 ASN C 57 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN A 38 ASN A 85 ASN E 53 GLN E 56 ASN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 0 HIS ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN F 62 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN H 111 HIS H 119 GLN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 ASN ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 0 HIS ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN D 108 GLN K 7 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.048257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.037144 restraints weight = 129875.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.038045 restraints weight = 67921.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.038640 restraints weight = 44955.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.039022 restraints weight = 34195.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.039234 restraints weight = 28671.512| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 16052 Z= 0.319 Angle : 0.855 12.052 22570 Z= 0.470 Chirality : 0.048 0.189 2562 Planarity : 0.005 0.043 2195 Dihedral : 30.933 167.657 3905 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 25.34 Ramachandran Plot: Outliers : 1.49 % Allowed : 17.45 % Favored : 81.06 % Rotamer: Outliers : 9.48 % Allowed : 19.76 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.21), residues: 1341 helix: -1.08 (0.21), residues: 495 sheet: -1.77 (0.29), residues: 335 loop : -3.43 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 34 TYR 0.020 0.002 TYR B 51 PHE 0.028 0.003 PHE A 52 TRP 0.020 0.003 TRP H 115 HIS 0.005 0.001 HIS E 111 Details of bonding type rmsd covalent geometry : bond 0.00699 (16052) covalent geometry : angle 0.85466 (22570) hydrogen bonds : bond 0.07706 ( 625) hydrogen bonds : angle 6.05381 ( 1539) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 177 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 132 THR cc_start: 0.9613 (OUTLIER) cc_final: 0.9126 (p) REVERT: A 29 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7707 (p) REVERT: A 49 GLU cc_start: 0.8745 (mp0) cc_final: 0.8410 (mp0) REVERT: E 3 LEU cc_start: 0.8394 (mt) cc_final: 0.8111 (mt) REVERT: E 106 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8214 (mp) REVERT: F 81 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6413 (pt) REVERT: H 49 GLU cc_start: 0.8319 (mp0) cc_final: 0.8090 (mp0) REVERT: H 106 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8911 (mt) REVERT: H 118 VAL cc_start: 0.9421 (OUTLIER) cc_final: 0.9147 (p) REVERT: H 133 VAL cc_start: 0.9308 (t) cc_final: 0.9059 (t) REVERT: H 137 MET cc_start: 0.8478 (mmm) cc_final: 0.7515 (mmp) REVERT: I 49 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8337 (tm-30) REVERT: I 53 GLN cc_start: 0.9438 (mm-40) cc_final: 0.9152 (mm-40) REVERT: I 109 PHE cc_start: 0.7422 (t80) cc_final: 0.6671 (t80) REVERT: J 6 PHE cc_start: 0.8771 (m-80) cc_final: 0.8261 (m-10) REVERT: J 41 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7913 (mt-10) REVERT: J 77 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7676 (m110) REVERT: J 86 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7069 (mtp85) REVERT: J 98 LYS cc_start: 0.9477 (tppt) cc_final: 0.9152 (tptp) REVERT: B 86 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.6842 (mtp85) REVERT: D 48 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8824 (t80) REVERT: D 109 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7944 (t80) REVERT: K 136 ARG cc_start: 0.8713 (ptm160) cc_final: 0.8430 (ptm-80) outliers start: 119 outliers final: 65 residues processed: 276 average time/residue: 0.1275 time to fit residues: 51.4440 Evaluate side-chains 217 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 141 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 77 ASN Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 13 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 133 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 ASN I 92 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN D 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.050029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.039106 restraints weight = 130499.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.040043 restraints weight = 67677.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.040633 restraints weight = 44604.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.040991 restraints weight = 34065.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.041253 restraints weight = 28769.088| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16052 Z= 0.174 Angle : 0.752 11.158 22570 Z= 0.419 Chirality : 0.044 0.212 2562 Planarity : 0.004 0.047 2195 Dihedral : 30.721 164.058 3868 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 1.57 % Allowed : 16.03 % Favored : 82.40 % Rotamer: Outliers : 6.85 % Allowed : 22.31 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.22), residues: 1341 helix: -0.68 (0.23), residues: 491 sheet: -1.49 (0.29), residues: 328 loop : -3.36 (0.23), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 34 TYR 0.013 0.001 TYR J 120 PHE 0.028 0.002 PHE A 52 TRP 0.015 0.002 TRP I 115 HIS 0.004 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00384 (16052) covalent geometry : angle 0.75227 (22570) hydrogen bonds : bond 0.05459 ( 625) hydrogen bonds : angle 5.53841 ( 1539) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 189 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8426 (mm-40) REVERT: A 33 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7571 (m-40) REVERT: A 49 GLU cc_start: 0.8645 (mp0) cc_final: 0.8353 (mp0) REVERT: A 55 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7783 (t80) REVERT: F 61 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8312 (p) REVERT: F 81 LEU cc_start: 0.6036 (OUTLIER) cc_final: 0.5716 (pt) REVERT: H 49 GLU cc_start: 0.8406 (mp0) cc_final: 0.8147 (mp0) REVERT: H 106 ILE cc_start: 0.9013 (mm) cc_final: 0.8701 (mt) REVERT: I 6 PHE cc_start: 0.7878 (m-80) cc_final: 0.7445 (m-80) REVERT: I 49 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8187 (tm-30) REVERT: I 53 GLN cc_start: 0.9543 (mm-40) cc_final: 0.9209 (mm-40) REVERT: I 93 LEU cc_start: 0.8587 (mt) cc_final: 0.8102 (mt) REVERT: J 6 PHE cc_start: 0.8932 (m-80) cc_final: 0.8693 (m-80) REVERT: J 25 PHE cc_start: 0.8740 (t80) cc_final: 0.8403 (t80) REVERT: J 30 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7377 (mm) REVERT: J 41 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7580 (mt-10) REVERT: J 86 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6786 (mmm-85) REVERT: J 98 LYS cc_start: 0.9449 (tppt) cc_final: 0.9097 (tppt) REVERT: J 108 GLN cc_start: 0.6874 (tp40) cc_final: 0.6642 (mm-40) REVERT: B 55 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8691 (t80) REVERT: B 86 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.6919 (mtp85) REVERT: B 95 SER cc_start: 0.9378 (t) cc_final: 0.9175 (p) REVERT: B 115 TRP cc_start: 0.7902 (OUTLIER) cc_final: 0.6840 (t60) REVERT: D 23 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8176 (tpm-80) REVERT: D 48 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8455 (t80) REVERT: K 136 ARG cc_start: 0.8676 (ptm160) cc_final: 0.8442 (ptm-80) outliers start: 86 outliers final: 45 residues processed: 264 average time/residue: 0.1245 time to fit residues: 47.8828 Evaluate side-chains 210 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 153 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 31 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.048568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.037641 restraints weight = 130402.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.038555 restraints weight = 67665.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.039153 restraints weight = 44677.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.039535 restraints weight = 33929.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.039736 restraints weight = 28514.847| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16052 Z= 0.227 Angle : 0.766 10.750 22570 Z= 0.424 Chirality : 0.044 0.191 2562 Planarity : 0.004 0.046 2195 Dihedral : 30.613 166.668 3842 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 1.49 % Allowed : 17.45 % Favored : 81.06 % Rotamer: Outliers : 7.65 % Allowed : 23.19 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.22), residues: 1341 helix: -0.55 (0.23), residues: 486 sheet: -1.50 (0.29), residues: 330 loop : -3.26 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 70 TYR 0.014 0.002 TYR B 51 PHE 0.028 0.002 PHE A 52 TRP 0.013 0.002 TRP H 115 HIS 0.005 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00506 (16052) covalent geometry : angle 0.76555 (22570) hydrogen bonds : bond 0.06140 ( 625) hydrogen bonds : angle 5.49443 ( 1539) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 165 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8374 (mm-40) REVERT: A 33 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7664 (m-40) REVERT: A 49 GLU cc_start: 0.8690 (mp0) cc_final: 0.8366 (mp0) REVERT: A 70 ARG cc_start: 0.8110 (ttt180) cc_final: 0.7892 (ttt180) REVERT: E 106 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8198 (mp) REVERT: F 49 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8857 (mm-30) REVERT: H 77 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.7792 (m110) REVERT: H 106 ILE cc_start: 0.9052 (mm) cc_final: 0.8761 (mt) REVERT: H 118 VAL cc_start: 0.9415 (OUTLIER) cc_final: 0.9138 (p) REVERT: I 6 PHE cc_start: 0.7893 (m-80) cc_final: 0.7478 (m-80) REVERT: I 93 LEU cc_start: 0.8697 (mt) cc_final: 0.8295 (mt) REVERT: I 109 PHE cc_start: 0.7401 (t80) cc_final: 0.6667 (t80) REVERT: I 120 TYR cc_start: 0.9067 (t80) cc_final: 0.8592 (t80) REVERT: J 6 PHE cc_start: 0.8901 (m-80) cc_final: 0.8170 (m-10) REVERT: J 25 PHE cc_start: 0.8685 (t80) cc_final: 0.8464 (t80) REVERT: J 41 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7922 (mt-10) REVERT: J 86 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6913 (mmm-85) REVERT: J 98 LYS cc_start: 0.9477 (tppt) cc_final: 0.9102 (tppt) REVERT: B 55 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8748 (t80) REVERT: B 86 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.6867 (mtp85) REVERT: B 115 TRP cc_start: 0.8126 (OUTLIER) cc_final: 0.6830 (t60) REVERT: D 23 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8034 (tpm-80) REVERT: D 48 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8782 (t80) REVERT: D 58 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7544 (p90) REVERT: K 121 GLU cc_start: 0.9466 (tp30) cc_final: 0.9105 (tp30) REVERT: K 136 ARG cc_start: 0.8762 (ptm160) cc_final: 0.8476 (ptm-80) outliers start: 96 outliers final: 59 residues processed: 245 average time/residue: 0.1268 time to fit residues: 45.5700 Evaluate side-chains 215 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 144 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN A 119 GLN E 111 HIS ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 HIS B 38 ASN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.049327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.038370 restraints weight = 130483.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.039295 restraints weight = 68320.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.039884 restraints weight = 45245.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.040275 restraints weight = 34561.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.040453 restraints weight = 29047.389| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16052 Z= 0.184 Angle : 0.739 9.545 22570 Z= 0.411 Chirality : 0.044 0.235 2562 Planarity : 0.004 0.049 2195 Dihedral : 30.456 167.669 3842 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 1.49 % Allowed : 15.44 % Favored : 83.07 % Rotamer: Outliers : 6.37 % Allowed : 24.94 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.22), residues: 1341 helix: -0.40 (0.23), residues: 497 sheet: -1.28 (0.29), residues: 331 loop : -3.27 (0.23), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 70 TYR 0.011 0.001 TYR B 51 PHE 0.029 0.002 PHE A 52 TRP 0.014 0.002 TRP H 115 HIS 0.009 0.001 HIS J 111 Details of bonding type rmsd covalent geometry : bond 0.00413 (16052) covalent geometry : angle 0.73940 (22570) hydrogen bonds : bond 0.05219 ( 625) hydrogen bonds : angle 5.28598 ( 1539) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 170 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8410 (mm-40) REVERT: A 33 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7595 (m-40) REVERT: A 49 GLU cc_start: 0.8640 (mp0) cc_final: 0.8261 (mp0) REVERT: A 120 TYR cc_start: 0.8433 (t80) cc_final: 0.8232 (t80) REVERT: E 106 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8142 (mp) REVERT: H 77 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.7649 (m110) REVERT: H 106 ILE cc_start: 0.8990 (mm) cc_final: 0.8748 (mt) REVERT: I 6 PHE cc_start: 0.7909 (m-80) cc_final: 0.7501 (m-80) REVERT: I 44 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8881 (ttmt) REVERT: I 55 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: I 92 ASN cc_start: 0.9322 (OUTLIER) cc_final: 0.8895 (p0) REVERT: I 93 LEU cc_start: 0.8709 (mt) cc_final: 0.8282 (mt) REVERT: J 6 PHE cc_start: 0.8992 (m-80) cc_final: 0.8181 (m-10) REVERT: J 41 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7832 (mt-10) REVERT: J 86 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6865 (mmm-85) REVERT: J 98 LYS cc_start: 0.9449 (tppt) cc_final: 0.9077 (tppt) REVERT: B 27 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8580 (p0) REVERT: B 55 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.8759 (t80) REVERT: B 86 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.6913 (mtp85) REVERT: B 115 TRP cc_start: 0.7797 (OUTLIER) cc_final: 0.7113 (t60) REVERT: D 23 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8108 (tpm-80) REVERT: D 30 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8598 (mm) REVERT: D 48 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8716 (t80) REVERT: D 58 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7572 (p90) REVERT: K 121 GLU cc_start: 0.9456 (tp30) cc_final: 0.9094 (tp30) REVERT: K 136 ARG cc_start: 0.8786 (ptm160) cc_final: 0.8514 (ptm-80) outliers start: 80 outliers final: 51 residues processed: 238 average time/residue: 0.1312 time to fit residues: 45.4920 Evaluate side-chains 209 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 142 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 55 PHE Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain K residue 87 ILE Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 78 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.049422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.038458 restraints weight = 130728.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.039386 restraints weight = 68399.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.039973 restraints weight = 45391.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.040370 restraints weight = 34803.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.040578 restraints weight = 29125.446| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16052 Z= 0.178 Angle : 0.740 8.911 22570 Z= 0.409 Chirality : 0.043 0.253 2562 Planarity : 0.004 0.053 2195 Dihedral : 30.322 171.143 3838 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 1.34 % Allowed : 15.96 % Favored : 82.70 % Rotamer: Outliers : 6.45 % Allowed : 26.22 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.22), residues: 1341 helix: -0.27 (0.23), residues: 498 sheet: -1.20 (0.30), residues: 318 loop : -3.28 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 70 TYR 0.012 0.001 TYR B 51 PHE 0.033 0.001 PHE I 48 TRP 0.016 0.002 TRP H 115 HIS 0.005 0.001 HIS E 111 Details of bonding type rmsd covalent geometry : bond 0.00400 (16052) covalent geometry : angle 0.73964 (22570) hydrogen bonds : bond 0.05151 ( 625) hydrogen bonds : angle 5.18301 ( 1539) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 163 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8414 (mm-40) REVERT: A 49 GLU cc_start: 0.8632 (mp0) cc_final: 0.8234 (mp0) REVERT: A 55 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7918 (t80) REVERT: E 106 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8179 (mp) REVERT: H 77 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.7684 (m110) REVERT: H 106 ILE cc_start: 0.9042 (mm) cc_final: 0.8823 (mt) REVERT: I 6 PHE cc_start: 0.7908 (m-80) cc_final: 0.7539 (m-80) REVERT: I 55 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: I 92 ASN cc_start: 0.9305 (OUTLIER) cc_final: 0.8906 (p0) REVERT: I 93 LEU cc_start: 0.8709 (mt) cc_final: 0.8036 (mt) REVERT: J 6 PHE cc_start: 0.9062 (m-80) cc_final: 0.8175 (m-10) REVERT: J 41 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7881 (mt-10) REVERT: J 86 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6910 (mmm-85) REVERT: J 98 LYS cc_start: 0.9446 (tppt) cc_final: 0.9077 (tppt) REVERT: B 27 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8619 (p0) REVERT: B 55 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8732 (t80) REVERT: B 86 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.6951 (mtp85) REVERT: B 115 TRP cc_start: 0.7633 (OUTLIER) cc_final: 0.6942 (t60) REVERT: D 23 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8081 (tpm-80) REVERT: D 30 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8604 (mm) REVERT: D 48 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8720 (t80) REVERT: D 58 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7652 (p90) REVERT: K 121 GLU cc_start: 0.9463 (tp30) cc_final: 0.9096 (tp30) REVERT: K 136 ARG cc_start: 0.8764 (ptm160) cc_final: 0.8482 (ptm-80) outliers start: 81 outliers final: 55 residues processed: 232 average time/residue: 0.1240 time to fit residues: 42.2871 Evaluate side-chains 207 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 137 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 55 PHE Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 124 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN D 53 GLN K 7 ASN ** K 108 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 = 0.3521 r_free = 0.3521 target = 0.047555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.036505 restraints weight = 132876.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.037372 restraints weight = 71549.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.037920 restraints weight = 48227.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.038277 restraints weight = 37572.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.038463 restraints weight = 31895.633| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 16052 Z= 0.270 Angle : 0.788 8.443 22570 Z= 0.434 Chirality : 0.045 0.240 2562 Planarity : 0.005 0.054 2195 Dihedral : 30.462 173.044 3838 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 1.27 % Allowed : 18.12 % Favored : 80.61 % Rotamer: Outliers : 7.09 % Allowed : 26.61 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.22), residues: 1341 helix: -0.49 (0.23), residues: 507 sheet: -1.46 (0.30), residues: 301 loop : -3.23 (0.23), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 15 TYR 0.015 0.002 TYR B 51 PHE 0.035 0.002 PHE I 48 TRP 0.017 0.002 TRP H 115 HIS 0.007 0.001 HIS K 0 Details of bonding type rmsd covalent geometry : bond 0.00598 (16052) covalent geometry : angle 0.78766 (22570) hydrogen bonds : bond 0.06607 ( 625) hydrogen bonds : angle 5.52852 ( 1539) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 134 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8541 (mp0) cc_final: 0.8174 (mp0) REVERT: H 63 LYS cc_start: 0.9282 (mmmt) cc_final: 0.9036 (mmmt) REVERT: I 6 PHE cc_start: 0.7862 (m-80) cc_final: 0.7506 (m-80) REVERT: I 44 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8974 (mttt) REVERT: I 93 LEU cc_start: 0.8752 (mt) cc_final: 0.8204 (mt) REVERT: I 119 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8569 (mt0) REVERT: J 6 PHE cc_start: 0.9099 (m-80) cc_final: 0.8171 (m-10) REVERT: J 41 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8014 (mt-10) REVERT: J 86 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7060 (mmm-85) REVERT: J 98 LYS cc_start: 0.9449 (tppt) cc_final: 0.9027 (tppt) REVERT: B 27 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8584 (p0) REVERT: B 55 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8605 (t80) REVERT: B 86 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.6865 (mtp85) REVERT: B 115 TRP cc_start: 0.8162 (OUTLIER) cc_final: 0.7119 (t60) REVERT: D 23 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7810 (tpt-90) REVERT: K 80 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8312 (mm-30) REVERT: K 121 GLU cc_start: 0.9500 (tp30) cc_final: 0.9133 (tp30) REVERT: K 136 ARG cc_start: 0.8804 (ptm160) cc_final: 0.8534 (ptm-80) outliers start: 89 outliers final: 63 residues processed: 210 average time/residue: 0.1256 time to fit residues: 38.9910 Evaluate side-chains 196 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 125 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 72 ILE Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain K residue 12 ASN Chi-restraints excluded: chain K residue 87 ILE Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 65 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 111 HIS ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** K 108 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 = 0.3569 r_free = 0.3569 target = 0.049317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.038335 restraints weight = 132474.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.039270 restraints weight = 68780.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.039868 restraints weight = 45546.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.040248 restraints weight = 34745.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.040450 restraints weight = 29297.143| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16052 Z= 0.169 Angle : 0.759 8.730 22570 Z= 0.419 Chirality : 0.044 0.248 2562 Planarity : 0.004 0.045 2195 Dihedral : 30.238 171.928 3833 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 1.19 % Allowed : 15.29 % Favored : 83.52 % Rotamer: Outliers : 5.82 % Allowed : 27.73 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.22), residues: 1341 helix: -0.38 (0.23), residues: 506 sheet: -1.41 (0.31), residues: 293 loop : -3.22 (0.22), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 15 TYR 0.011 0.001 TYR F 120 PHE 0.032 0.001 PHE A 52 TRP 0.018 0.002 TRP H 115 HIS 0.006 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00380 (16052) covalent geometry : angle 0.75924 (22570) hydrogen bonds : bond 0.05015 ( 625) hydrogen bonds : angle 5.18944 ( 1539) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 160 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8521 (mp0) cc_final: 0.8120 (mp0) REVERT: A 55 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7914 (t80) REVERT: H 63 LYS cc_start: 0.9287 (mmmt) cc_final: 0.9062 (mmmt) REVERT: H 77 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.7666 (m110) REVERT: I 6 PHE cc_start: 0.7868 (m-80) cc_final: 0.7519 (m-80) REVERT: I 44 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8891 (mttt) REVERT: I 55 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7900 (m-80) REVERT: I 92 ASN cc_start: 0.9292 (OUTLIER) cc_final: 0.8853 (p0) REVERT: I 93 LEU cc_start: 0.8751 (mt) cc_final: 0.8202 (mt) REVERT: J 6 PHE cc_start: 0.9185 (m-80) cc_final: 0.8285 (m-10) REVERT: J 41 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7929 (mt-10) REVERT: J 86 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6975 (mmm-85) REVERT: J 98 LYS cc_start: 0.9384 (tppt) cc_final: 0.9018 (tppt) REVERT: B 27 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8597 (p0) REVERT: B 55 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8701 (t80) REVERT: B 86 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7539 (mtm-85) REVERT: B 115 TRP cc_start: 0.7654 (OUTLIER) cc_final: 0.7213 (t60) REVERT: D 1 MET cc_start: 0.8170 (mmm) cc_final: 0.7089 (mmm) REVERT: D 23 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8157 (tpm-80) REVERT: D 30 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8595 (mm) REVERT: K 80 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8273 (mm-30) REVERT: K 121 GLU cc_start: 0.9473 (tp30) cc_final: 0.9157 (tp30) REVERT: K 136 ARG cc_start: 0.8784 (ptm160) cc_final: 0.8480 (ptm-80) outliers start: 73 outliers final: 48 residues processed: 220 average time/residue: 0.1305 time to fit residues: 41.5384 Evaluate side-chains 196 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 136 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 55 PHE Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain K residue 87 ILE Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 3 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 14 optimal weight: 0.0570 chunk 36 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 14 ASN ** I 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN D 53 GLN ** K 122 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 = 0.3554 r_free = 0.3554 target = 0.048749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.037707 restraints weight = 133083.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.038626 restraints weight = 69284.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.039217 restraints weight = 46071.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.039597 restraints weight = 35318.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.039769 restraints weight = 29750.294| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16052 Z= 0.198 Angle : 0.773 9.315 22570 Z= 0.428 Chirality : 0.044 0.317 2562 Planarity : 0.005 0.048 2195 Dihedral : 30.201 173.769 3825 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 1.19 % Allowed : 16.03 % Favored : 82.77 % Rotamer: Outliers : 4.94 % Allowed : 29.08 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.22), residues: 1341 helix: -0.55 (0.22), residues: 520 sheet: -1.47 (0.31), residues: 294 loop : -3.29 (0.22), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 70 TYR 0.013 0.001 TYR K 120 PHE 0.032 0.002 PHE A 52 TRP 0.012 0.002 TRP H 115 HIS 0.005 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00445 (16052) covalent geometry : angle 0.77291 (22570) hydrogen bonds : bond 0.05441 ( 625) hydrogen bonds : angle 5.26917 ( 1539) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 139 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8564 (mp0) cc_final: 0.8130 (mp0) REVERT: A 55 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7954 (t80) REVERT: H 63 LYS cc_start: 0.9319 (mmmt) cc_final: 0.9030 (mmmt) REVERT: H 77 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7657 (m110) REVERT: I 1 MET cc_start: 0.7690 (tpt) cc_final: 0.7414 (tpp) REVERT: I 6 PHE cc_start: 0.7891 (m-80) cc_final: 0.7525 (m-80) REVERT: I 44 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8947 (tttt) REVERT: I 92 ASN cc_start: 0.9252 (OUTLIER) cc_final: 0.8782 (p0) REVERT: I 93 LEU cc_start: 0.8797 (mt) cc_final: 0.8172 (mt) REVERT: J 6 PHE cc_start: 0.9210 (m-80) cc_final: 0.8268 (m-10) REVERT: J 41 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8004 (mt-10) REVERT: J 86 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7070 (mmm-85) REVERT: J 98 LYS cc_start: 0.9393 (tppt) cc_final: 0.9008 (tppt) REVERT: B 27 ASP cc_start: 0.8988 (OUTLIER) cc_final: 0.8619 (p0) REVERT: B 55 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8706 (t80) REVERT: B 86 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.6962 (mtp85) REVERT: B 115 TRP cc_start: 0.7715 (OUTLIER) cc_final: 0.7076 (t60) REVERT: D 1 MET cc_start: 0.8109 (mmm) cc_final: 0.7344 (mmm) REVERT: D 23 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8104 (tpm-80) REVERT: D 30 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8635 (mm) REVERT: K 80 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8300 (mm-30) REVERT: K 121 GLU cc_start: 0.9368 (tp30) cc_final: 0.9131 (tp30) REVERT: K 136 ARG cc_start: 0.8817 (ptm160) cc_final: 0.8497 (ptm-80) outliers start: 62 outliers final: 49 residues processed: 192 average time/residue: 0.1239 time to fit residues: 34.9258 Evaluate side-chains 190 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 130 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain K residue 87 ILE Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 10 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 90 optimal weight: 0.0040 chunk 74 optimal weight: 0.0570 chunk 120 optimal weight: 0.2980 chunk 131 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 overall best weight: 0.3710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 38 ASN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 GLN ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN D 119 GLN ** K 122 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 = 0.3605 r_free = 0.3605 target = 0.050592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.039817 restraints weight = 132100.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.040765 restraints weight = 68265.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.041357 restraints weight = 45034.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.041753 restraints weight = 34464.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.042010 restraints weight = 28901.680| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16052 Z= 0.165 Angle : 0.779 10.059 22570 Z= 0.430 Chirality : 0.044 0.272 2562 Planarity : 0.005 0.062 2195 Dihedral : 29.963 173.392 3825 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 1.12 % Allowed : 14.77 % Favored : 84.12 % Rotamer: Outliers : 4.78 % Allowed : 29.40 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.22), residues: 1341 helix: -0.48 (0.23), residues: 502 sheet: -1.31 (0.31), residues: 285 loop : -3.09 (0.22), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 15 TYR 0.011 0.001 TYR B 51 PHE 0.027 0.001 PHE A 52 TRP 0.016 0.002 TRP E 115 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00367 (16052) covalent geometry : angle 0.77850 (22570) hydrogen bonds : bond 0.05086 ( 625) hydrogen bonds : angle 5.12044 ( 1539) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 168 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8510 (mp0) cc_final: 0.8130 (mp0) REVERT: E 44 LYS cc_start: 0.8908 (tttt) cc_final: 0.8578 (tptt) REVERT: F 63 LYS cc_start: 0.8925 (mmmt) cc_final: 0.8540 (tptt) REVERT: H 77 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7662 (m110) REVERT: I 6 PHE cc_start: 0.7830 (m-80) cc_final: 0.7594 (m-80) REVERT: I 44 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8888 (tttt) REVERT: I 92 ASN cc_start: 0.9249 (OUTLIER) cc_final: 0.8808 (p0) REVERT: I 93 LEU cc_start: 0.8736 (mt) cc_final: 0.8222 (mt) REVERT: J 6 PHE cc_start: 0.9160 (m-80) cc_final: 0.8222 (m-80) REVERT: J 41 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8008 (mt-10) REVERT: J 63 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8206 (tppt) REVERT: J 86 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.6935 (mmm-85) REVERT: J 98 LYS cc_start: 0.9309 (tppt) cc_final: 0.8990 (tppt) REVERT: J 135 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8353 (mm-30) REVERT: B 72 ILE cc_start: 0.9161 (mm) cc_final: 0.8939 (tt) REVERT: B 86 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7349 (mtm-85) REVERT: D 1 MET cc_start: 0.7978 (mmm) cc_final: 0.6988 (mmm) REVERT: D 23 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8039 (tpm-80) REVERT: D 30 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8494 (mm) REVERT: K 80 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8201 (mm-30) REVERT: K 121 GLU cc_start: 0.9380 (tp30) cc_final: 0.9124 (tm-30) REVERT: K 136 ARG cc_start: 0.8860 (ptm160) cc_final: 0.8610 (ptm-80) outliers start: 60 outliers final: 39 residues processed: 219 average time/residue: 0.1294 time to fit residues: 41.0949 Evaluate side-chains 188 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 77 ASN Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain J residue 63 LYS Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain K residue 87 ILE Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** 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 = 0.3599 r_free = 0.3599 target = 0.050163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.039430 restraints weight = 136191.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.040370 restraints weight = 70587.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.040959 restraints weight = 46700.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.041339 restraints weight = 35758.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.041595 restraints weight = 30033.381| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.6058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16052 Z= 0.175 Angle : 0.785 11.183 22570 Z= 0.435 Chirality : 0.044 0.236 2562 Planarity : 0.005 0.057 2195 Dihedral : 29.897 175.286 3815 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 1.04 % Allowed : 15.73 % Favored : 83.22 % Rotamer: Outliers : 3.90 % Allowed : 30.84 % Favored : 65.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.22), residues: 1341 helix: -0.54 (0.23), residues: 512 sheet: -1.33 (0.30), residues: 295 loop : -3.18 (0.22), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 70 TYR 0.021 0.001 TYR J 51 PHE 0.025 0.001 PHE I 48 TRP 0.016 0.002 TRP H 115 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00395 (16052) covalent geometry : angle 0.78531 (22570) hydrogen bonds : bond 0.05154 ( 625) hydrogen bonds : angle 5.20245 ( 1539) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2728.24 seconds wall clock time: 47 minutes 49.70 seconds (2869.70 seconds total)