Starting phenix.real_space_refine on Sun Apr 5 13:39:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cg0_30348/04_2026/7cg0_30348.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cg0_30348/04_2026/7cg0_30348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cg0_30348/04_2026/7cg0_30348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cg0_30348/04_2026/7cg0_30348.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cg0_30348/04_2026/7cg0_30348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cg0_30348/04_2026/7cg0_30348.map" } resolution = 3.2 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= 0.002 sd= 0.066 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 6791 2.51 5 N 1925 2.21 5 O 2157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10928 Number of models: 1 Model: "" Number of chains: 21 Chain: "0" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "1" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "2" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "3" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "4" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "5" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "6" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "7" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "9" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "f" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 936 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain breaks: 1 Chain: "g" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 949 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain breaks: 1 Chain: "h" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 935 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain breaks: 1 Chain: "j" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 931 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain breaks: 1 Chain: "l" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 833 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "m" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 833 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "o" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 856 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain breaks: 1 Chain: "p" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 940 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain breaks: 1 Chain: "8" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 140 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 6, 'TRANS': 14} Chain: "i" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 944 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain breaks: 1 Chain: "k" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 852 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain breaks: 1 Chain: "n" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 844 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 1 Time building chain proxies: 2.58, per 1000 atoms: 0.24 Number of scatterers: 10928 At special positions: 0 Unit cell: (108.481, 111.095, 129.393, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 2157 8.00 N 1925 7.00 C 6791 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: 0.88 Conformation dependent library (CDL) restraints added in 400.9 milliseconds 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2798 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 17 sheets defined 53.5% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'f' and resid 4 through 30 removed outlier: 4.061A pdb=" N ASP f 8 " --> pdb=" O LEU f 4 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 33 No H-bonds generated for 'chain 'f' and resid 31 through 33' Processing helix chain 'f' and resid 97 through 130 removed outlier: 3.782A pdb=" N LEU f 130 " --> pdb=" O MET f 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 4 through 30 removed outlier: 3.881A pdb=" N ASP g 8 " --> pdb=" O LEU g 4 " (cutoff:3.500A) Processing helix chain 'g' and resid 36 through 40 removed outlier: 3.670A pdb=" N GLN g 40 " --> pdb=" O PRO g 37 " (cutoff:3.500A) Processing helix chain 'g' and resid 97 through 130 removed outlier: 3.742A pdb=" N LEU g 130 " --> pdb=" O MET g 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 131 through 134 removed outlier: 4.142A pdb=" N GLN g 134 " --> pdb=" O THR g 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 131 through 134' Processing helix chain 'h' and resid 4 through 30 removed outlier: 4.252A pdb=" N ASP h 8 " --> pdb=" O LEU h 4 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER h 12 " --> pdb=" O ASP h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 98 through 130 removed outlier: 3.927A pdb=" N MET h 106 " --> pdb=" O MET h 102 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 30 removed outlier: 4.042A pdb=" N PHE j 7 " --> pdb=" O LEU j 3 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP j 8 " --> pdb=" O LEU j 4 " (cutoff:3.500A) Processing helix chain 'j' and resid 31 through 33 No H-bonds generated for 'chain 'j' and resid 31 through 33' Processing helix chain 'j' and resid 98 through 131 removed outlier: 3.548A pdb=" N MET j 106 " --> pdb=" O MET j 102 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR j 131 " --> pdb=" O LEU j 127 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 32 removed outlier: 3.614A pdb=" N LEU l 9 " --> pdb=" O LEU l 5 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE l 11 " --> pdb=" O ALA l 7 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLN l 12 " --> pdb=" O ALA l 8 " (cutoff:3.500A) Processing helix chain 'l' and resid 44 through 54 Processing helix chain 'l' and resid 101 through 133 Processing helix chain 'm' and resid 4 through 32 removed outlier: 4.607A pdb=" N GLN m 12 " --> pdb=" O ALA m 8 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 54 Processing helix chain 'm' and resid 102 through 134 removed outlier: 3.693A pdb=" N VAL m 133 " --> pdb=" O GLY m 129 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU m 134 " --> pdb=" O MET m 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 32 removed outlier: 4.665A pdb=" N GLN o 12 " --> pdb=" O ALA o 8 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA o 15 " --> pdb=" O PHE o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 44 through 55 Processing helix chain 'o' and resid 101 through 134 removed outlier: 3.716A pdb=" N VAL o 133 " --> pdb=" O GLY o 129 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU o 134 " --> pdb=" O MET o 130 " (cutoff:3.500A) Processing helix chain 'p' and resid 4 through 30 removed outlier: 4.033A pdb=" N ASP p 8 " --> pdb=" O LEU p 4 " (cutoff:3.500A) Processing helix chain 'p' and resid 36 through 40 removed outlier: 3.867A pdb=" N GLN p 40 " --> pdb=" O PRO p 37 " (cutoff:3.500A) Processing helix chain 'p' and resid 97 through 131 Processing helix chain 'i' and resid 4 through 30 removed outlier: 4.178A pdb=" N ASP i 8 " --> pdb=" O LEU i 4 " (cutoff:3.500A) Processing helix chain 'i' and resid 97 through 130 Processing helix chain 'k' and resid 3 through 32 removed outlier: 3.993A pdb=" N ALA k 8 " --> pdb=" O ARG k 4 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU k 9 " --> pdb=" O LEU k 5 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE k 11 " --> pdb=" O ALA k 7 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N GLN k 12 " --> pdb=" O ALA k 8 " (cutoff:3.500A) Processing helix chain 'k' and resid 44 through 53 Processing helix chain 'k' and resid 102 through 134 removed outlier: 3.613A pdb=" N LEU k 134 " --> pdb=" O MET k 130 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 32 removed outlier: 4.340A pdb=" N GLN n 12 " --> pdb=" O ALA n 8 " (cutoff:3.500A) Processing helix chain 'n' and resid 44 through 55 removed outlier: 3.612A pdb=" N VAL n 54 " --> pdb=" O LYS n 50 " (cutoff:3.500A) Processing helix chain 'n' and resid 101 through 134 removed outlier: 3.751A pdb=" N LEU n 134 " --> pdb=" O MET n 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '5' and resid 316 through 317 Processing sheet with id=AA2, first strand: chain '6' and resid 316 through 317 Processing sheet with id=AA3, first strand: chain '7' and resid 316 through 317 Processing sheet with id=AA4, first strand: chain '9' and resid 316 through 317 Processing sheet with id=AA5, first strand: chain 'f' and resid 45 through 52 removed outlier: 6.255A pdb=" N GLN f 46 " --> pdb=" O VAL f 67 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL f 67 " --> pdb=" O GLN f 46 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL f 48 " --> pdb=" O ALA f 65 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY f 61 " --> pdb=" O ASP f 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 75 through 78 Processing sheet with id=AA7, first strand: chain 'g' and resid 45 through 51 removed outlier: 4.237A pdb=" N VAL g 48 " --> pdb=" O SER g 66 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N SER g 66 " --> pdb=" O VAL g 48 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLN g 50 " --> pdb=" O VAL g 64 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL g 64 " --> pdb=" O GLN g 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'g' and resid 75 through 78 Processing sheet with id=AA9, first strand: chain 'h' and resid 45 through 51 removed outlier: 6.315A pdb=" N GLN h 46 " --> pdb=" O VAL h 67 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL h 67 " --> pdb=" O GLN h 46 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL h 48 " --> pdb=" O ALA h 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'h' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'j' and resid 45 through 51 removed outlier: 4.042A pdb=" N SER j 66 " --> pdb=" O VAL j 48 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN j 50 " --> pdb=" O VAL j 64 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL j 64 " --> pdb=" O GLN j 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'j' and resid 76 through 78 Processing sheet with id=AB4, first strand: chain 'p' and resid 45 through 51 removed outlier: 6.348A pdb=" N GLN p 46 " --> pdb=" O VAL p 67 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL p 67 " --> pdb=" O GLN p 46 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL p 48 " --> pdb=" O ALA p 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'p' and resid 75 through 78 Processing sheet with id=AB6, first strand: chain 'i' and resid 45 through 51 removed outlier: 6.231A pdb=" N GLN i 46 " --> pdb=" O VAL i 67 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL i 67 " --> pdb=" O GLN i 46 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL i 48 " --> pdb=" O ALA i 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'i' and resid 76 through 78 Processing sheet with id=AB8, first strand: chain 'n' and resid 41 through 42 653 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.44 Time building geometry restraints manager: 1.17 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: 2506 1.33 - 1.45: 1919 1.45 - 1.57: 6508 1.57 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 11043 Sorted by residual: bond pdb=" N SER 7 317 " pdb=" CA SER 7 317 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.26e-02 6.30e+03 9.20e+00 bond pdb=" N ASN 7 318 " pdb=" CA ASN 7 318 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.21e-02 6.83e+03 7.49e+00 bond pdb=" N MET f 125 " pdb=" CA MET f 125 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.33e+00 bond pdb=" N GLN 7 319 " pdb=" CA GLN 7 319 " ideal model delta sigma weight residual 1.452 1.493 -0.040 1.80e-02 3.09e+03 5.04e+00 bond pdb=" N LYS h 128 " pdb=" CA LYS h 128 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.23e-02 6.61e+03 4.98e+00 ... (remaining 11038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 14490 1.28 - 2.56: 370 2.56 - 3.85: 107 3.85 - 5.13: 12 5.13 - 6.41: 3 Bond angle restraints: 14982 Sorted by residual: angle pdb=" N PRO 7 320 " pdb=" CA PRO 7 320 " pdb=" C PRO 7 320 " ideal model delta sigma weight residual 111.34 117.75 -6.41 1.55e+00 4.16e-01 1.71e+01 angle pdb=" N ASN 7 318 " pdb=" CA ASN 7 318 " pdb=" C ASN 7 318 " ideal model delta sigma weight residual 111.28 115.54 -4.26 1.09e+00 8.42e-01 1.53e+01 angle pdb=" C SER 7 317 " pdb=" N ASN 7 318 " pdb=" CA ASN 7 318 " ideal model delta sigma weight residual 120.28 125.13 -4.85 1.34e+00 5.57e-01 1.31e+01 angle pdb=" CA ASN 7 318 " pdb=" C ASN 7 318 " pdb=" O ASN 7 318 " ideal model delta sigma weight residual 120.55 116.88 3.67 1.06e+00 8.90e-01 1.20e+01 angle pdb=" C PRO 7 320 " pdb=" CA PRO 7 320 " pdb=" CB PRO 7 320 " ideal model delta sigma weight residual 111.12 106.95 4.17 1.29e+00 6.01e-01 1.05e+01 ... (remaining 14977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 6481 17.85 - 35.70: 311 35.70 - 53.55: 61 53.55 - 71.40: 8 71.40 - 89.25: 6 Dihedral angle restraints: 6867 sinusoidal: 2575 harmonic: 4292 Sorted by residual: dihedral pdb=" CA VAL i 34 " pdb=" C VAL i 34 " pdb=" N THR i 35 " pdb=" CA THR i 35 " ideal model delta harmonic sigma weight residual 180.00 163.85 16.15 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA ASN i 22 " pdb=" CB ASN i 22 " pdb=" CG ASN i 22 " pdb=" OD1 ASN i 22 " ideal model delta sinusoidal sigma weight residual -90.00 -157.41 67.41 2 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" N LEU o 18 " pdb=" CA LEU o 18 " pdb=" CB LEU o 18 " pdb=" CG LEU o 18 " ideal model delta sinusoidal sigma weight residual -60.00 -118.68 58.68 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 6864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1118 0.030 - 0.059: 466 0.059 - 0.089: 128 0.089 - 0.118: 66 0.118 - 0.148: 5 Chirality restraints: 1783 Sorted by residual: chirality pdb=" CA MET f 125 " pdb=" N MET f 125 " pdb=" C MET f 125 " pdb=" CB MET f 125 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA THR g 35 " pdb=" N THR g 35 " pdb=" C THR g 35 " pdb=" CB THR g 35 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA THR p 35 " pdb=" N THR p 35 " pdb=" C THR p 35 " pdb=" CB THR p 35 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 1780 not shown) Planarity restraints: 2002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE g 116 " 0.013 2.00e-02 2.50e+03 2.50e-02 6.23e+00 pdb=" C ILE g 116 " -0.043 2.00e-02 2.50e+03 pdb=" O ILE g 116 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU g 117 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU g 117 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" C GLU g 117 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU g 117 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL g 118 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS h 128 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C LYS h 128 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS h 128 " 0.010 2.00e-02 2.50e+03 pdb=" N THR h 129 " 0.010 2.00e-02 2.50e+03 ... (remaining 1999 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 92 2.57 - 3.16: 9198 3.16 - 3.74: 16917 3.74 - 4.32: 19932 4.32 - 4.90: 34973 Nonbonded interactions: 81112 Sorted by model distance: nonbonded pdb=" O UNK 2 9 " pdb=" ND2 ASN i 104 " model vdw 1.992 3.120 nonbonded pdb=" OG1 THR 9 330 " pdb=" OD1 ASP j 38 " model vdw 2.155 3.040 nonbonded pdb=" OG SER h 12 " pdb=" O VAL h 62 " model vdw 2.172 3.040 nonbonded pdb=" OH TYR o 116 " pdb=" OG1 THR p 129 " model vdw 2.289 3.040 nonbonded pdb=" OD1 ASN h 27 " pdb=" OH TYR h 42 " model vdw 2.292 3.040 ... (remaining 81107 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 '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' } ncs_group { reference = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' } ncs_group { reference = (chain 'f' and (resid 2 through 53 or resid 59 through 132)) selection = (chain 'g' and (resid 2 through 53 or resid 59 through 132)) selection = (chain 'h' and (resid 2 through 53 or resid 59 through 132)) selection = (chain 'i' and (resid 2 through 53 or resid 59 through 132)) selection = (chain 'j' and (resid 2 through 53 or resid 59 through 132)) selection = (chain 'p' and (resid 2 through 53 or resid 59 through 132)) } ncs_group { reference = (chain 'k' and (resid 3 through 54 or resid 82 through 135)) selection = chain 'l' selection = chain 'm' selection = (chain 'n' and (resid 3 through 54 or resid 82 through 135)) selection = (chain 'o' and (resid 3 through 54 or resid 82 through 135)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.770 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.290 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 : 0.003 0.040 11043 Z= 0.165 Angle : 0.531 6.410 14982 Z= 0.282 Chirality : 0.038 0.148 1783 Planarity : 0.003 0.035 2002 Dihedral : 11.229 89.246 4069 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.56 % Allowed : 7.94 % Favored : 89.50 % 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: 3.52 (0.24), residues: 1358 helix: 4.00 (0.19), residues: 723 sheet: -2.02 (0.37), residues: 137 loop : 1.18 (0.31), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG k 106 TYR 0.014 0.001 TYR j 112 PHE 0.013 0.001 PHE o 11 Details of bonding type rmsd covalent geometry : bond 0.00337 (11043) covalent geometry : angle 0.53121 (14982) hydrogen bonds : bond 0.06647 ( 653) hydrogen bonds : angle 3.52286 ( 1926) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 561 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 21 LEU cc_start: 0.9397 (tp) cc_final: 0.9154 (tt) REVERT: f 43 ARG cc_start: 0.7893 (ptp-110) cc_final: 0.7685 (mtm-85) REVERT: f 123 LYS cc_start: 0.9039 (ttpt) cc_final: 0.8759 (tttt) REVERT: g 22 ASN cc_start: 0.8388 (m-40) cc_final: 0.8108 (m-40) REVERT: g 45 LYS cc_start: 0.7957 (ptpp) cc_final: 0.7606 (pttm) REVERT: g 106 MET cc_start: 0.8174 (tpp) cc_final: 0.7951 (mmm) REVERT: g 123 LYS cc_start: 0.8355 (tttp) cc_final: 0.8106 (ttpp) REVERT: h 97 ASP cc_start: 0.8681 (p0) cc_final: 0.8453 (p0) REVERT: h 102 MET cc_start: 0.8158 (mmm) cc_final: 0.7893 (mmm) REVERT: h 116 ILE cc_start: 0.9266 (mm) cc_final: 0.9026 (mt) REVERT: l 10 ARG cc_start: 0.7821 (ttt-90) cc_final: 0.7421 (ttp80) REVERT: l 12 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7899 (mm110) REVERT: l 17 ASN cc_start: 0.8463 (t0) cc_final: 0.8178 (t0) REVERT: l 106 ARG cc_start: 0.8574 (mtp180) cc_final: 0.7578 (mmm160) REVERT: l 131 MET cc_start: 0.8790 (tpp) cc_final: 0.8331 (tpp) REVERT: l 132 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8829 (t0) REVERT: l 133 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8758 (p) REVERT: m 4 ARG cc_start: 0.4391 (OUTLIER) cc_final: 0.4157 (mtt180) REVERT: m 5 LEU cc_start: 0.7069 (tp) cc_final: 0.6787 (tp) REVERT: m 14 GLU cc_start: 0.7373 (mp0) cc_final: 0.7155 (mp0) REVERT: m 23 GLN cc_start: 0.8949 (tp-100) cc_final: 0.8687 (tp40) REVERT: m 24 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7296 (tm-30) REVERT: m 25 ILE cc_start: 0.8915 (mt) cc_final: 0.8636 (mt) REVERT: m 41 ARG cc_start: 0.8783 (mmm-85) cc_final: 0.8543 (mmm-85) REVERT: m 87 TYR cc_start: 0.8478 (m-80) cc_final: 0.8126 (m-80) REVERT: o 104 ARG cc_start: 0.7809 (ttm-80) cc_final: 0.7463 (ttm-80) REVERT: o 107 THR cc_start: 0.8948 (m) cc_final: 0.8585 (p) REVERT: o 108 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8061 (mm-40) REVERT: o 115 LYS cc_start: 0.8432 (mmmm) cc_final: 0.7632 (mtmt) REVERT: p 9 ILE cc_start: 0.6650 (mm) cc_final: 0.6443 (tt) REVERT: i 74 GLU cc_start: 0.8007 (pm20) cc_final: 0.7381 (pm20) REVERT: k 24 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7758 (tm-30) REVERT: k 94 SER cc_start: 0.7974 (t) cc_final: 0.7482 (p) REVERT: k 106 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7195 (tpt170) REVERT: k 111 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8271 (p0) REVERT: k 128 LYS cc_start: 0.8079 (mttt) cc_final: 0.7667 (mttt) REVERT: k 130 MET cc_start: 0.8492 (tpp) cc_final: 0.8046 (tpp) REVERT: n 106 ARG cc_start: 0.8167 (mtm-85) cc_final: 0.7934 (mtm180) outliers start: 29 outliers final: 5 residues processed: 577 average time/residue: 0.1013 time to fit residues: 80.6905 Evaluate side-chains 453 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 444 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain h residue 128 LYS Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain l residue 132 ASN Chi-restraints excluded: chain l residue 133 VAL Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain k residue 111 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 30 ASN f 88 ASN g 27 ASN g 104 ASN g 113 GLN j 30 ASN l 21 GLN l 23 GLN m 32 ASN ** o 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 30 ASN p 104 ASN k 132 ASN n 17 ASN n 21 GLN n 112 ASN ** n 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.137167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.117682 restraints weight = 18519.556| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.68 r_work: 0.3497 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11043 Z= 0.135 Angle : 0.553 6.839 14982 Z= 0.277 Chirality : 0.039 0.161 1783 Planarity : 0.004 0.035 2002 Dihedral : 4.488 57.741 1574 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.80 % Allowed : 17.65 % Favored : 78.55 % 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: 3.37 (0.24), residues: 1358 helix: 3.85 (0.18), residues: 718 sheet: -1.64 (0.36), residues: 151 loop : 1.13 (0.31), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG f 43 TYR 0.018 0.001 TYR g 78 PHE 0.018 0.002 PHE o 45 Details of bonding type rmsd covalent geometry : bond 0.00301 (11043) covalent geometry : angle 0.55309 (14982) hydrogen bonds : bond 0.04096 ( 653) hydrogen bonds : angle 3.31590 ( 1926) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 470 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 70 SER cc_start: 0.7735 (OUTLIER) cc_final: 0.7500 (m) REVERT: f 123 LYS cc_start: 0.9070 (ttpt) cc_final: 0.8836 (tttt) REVERT: g 22 ASN cc_start: 0.8738 (m-40) cc_final: 0.8493 (m-40) REVERT: g 45 LYS cc_start: 0.8106 (ptpp) cc_final: 0.7763 (pttm) REVERT: g 123 LYS cc_start: 0.8722 (tttp) cc_final: 0.8371 (ttpp) REVERT: g 128 LYS cc_start: 0.8777 (ttpt) cc_final: 0.8381 (ttpt) REVERT: h 30 ASN cc_start: 0.9113 (m-40) cc_final: 0.8796 (m110) REVERT: h 116 ILE cc_start: 0.9471 (mm) cc_final: 0.9211 (mt) REVERT: h 128 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8989 (tptm) REVERT: l 12 GLN cc_start: 0.8243 (mm-40) cc_final: 0.8036 (mm110) REVERT: l 17 ASN cc_start: 0.8685 (t0) cc_final: 0.8389 (t0) REVERT: l 86 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8726 (pp) REVERT: l 115 LYS cc_start: 0.9093 (mtmt) cc_final: 0.8885 (mtpt) REVERT: l 131 MET cc_start: 0.8813 (tpp) cc_final: 0.8477 (tpp) REVERT: m 4 ARG cc_start: 0.4409 (OUTLIER) cc_final: 0.4053 (mtt180) REVERT: m 5 LEU cc_start: 0.7181 (tp) cc_final: 0.6940 (tp) REVERT: m 14 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: m 24 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7937 (tm-30) REVERT: m 25 ILE cc_start: 0.9379 (mt) cc_final: 0.9120 (mt) REVERT: m 41 ARG cc_start: 0.9041 (mmm-85) cc_final: 0.8804 (mmm-85) REVERT: m 87 TYR cc_start: 0.8668 (m-80) cc_final: 0.8446 (m-80) REVERT: m 96 ASP cc_start: 0.8408 (p0) cc_final: 0.8195 (p0) REVERT: m 130 MET cc_start: 0.9066 (tpp) cc_final: 0.8700 (tpp) REVERT: m 135 GLN cc_start: 0.7628 (mp10) cc_final: 0.6947 (mp10) REVERT: o 102 MET cc_start: 0.7410 (tpp) cc_final: 0.7053 (tmm) REVERT: o 104 ARG cc_start: 0.8146 (ttm-80) cc_final: 0.7759 (ttm-80) REVERT: o 107 THR cc_start: 0.9112 (m) cc_final: 0.8741 (p) REVERT: o 108 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8444 (mm-40) REVERT: o 115 LYS cc_start: 0.8852 (mmmm) cc_final: 0.8172 (mtmt) REVERT: o 132 ASN cc_start: 0.8567 (t0) cc_final: 0.8356 (t0) REVERT: p 9 ILE cc_start: 0.6922 (mm) cc_final: 0.6651 (tt) REVERT: p 102 MET cc_start: 0.8072 (mtt) cc_final: 0.7794 (mtt) REVERT: i 74 GLU cc_start: 0.8071 (pm20) cc_final: 0.7842 (pm20) REVERT: i 92 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8261 (mtpt) REVERT: i 102 MET cc_start: 0.8800 (mmm) cc_final: 0.8412 (mmm) REVERT: k 24 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8125 (tm-30) REVERT: k 111 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8547 (p0) REVERT: k 118 MET cc_start: 0.8991 (tmm) cc_final: 0.8776 (tmm) REVERT: k 128 LYS cc_start: 0.8271 (mttt) cc_final: 0.8054 (mttt) REVERT: k 130 MET cc_start: 0.8828 (tpp) cc_final: 0.8414 (tpp) REVERT: n 23 GLN cc_start: 0.8746 (tp-100) cc_final: 0.8456 (tp40) REVERT: n 106 ARG cc_start: 0.8570 (mtm-85) cc_final: 0.8240 (mtm180) REVERT: n 112 ASN cc_start: 0.8967 (OUTLIER) cc_final: 0.8672 (t0) outliers start: 43 outliers final: 19 residues processed: 489 average time/residue: 0.0984 time to fit residues: 66.8841 Evaluate side-chains 477 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 450 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 124 SER Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 128 LYS Chi-restraints excluded: chain j residue 34 VAL Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain l residue 83 VAL Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain l residue 114 LEU Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain m residue 14 GLU Chi-restraints excluded: chain m residue 125 SER Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 122 VAL Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain i residue 92 LYS Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 111 ASP Chi-restraints excluded: chain n residue 112 ASN Chi-restraints excluded: chain n residue 117 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 133 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 324 ASN f 22 ASN g 113 GLN g 115 ASN h 113 GLN j 30 ASN j 115 ASN l 108 GLN ** l 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN m 92 GLN o 29 ASN p 22 ASN ** i 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 32 ASN n 23 GLN ** n 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.132100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.111941 restraints weight = 18786.017| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.76 r_work: 0.3416 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11043 Z= 0.167 Angle : 0.564 7.950 14982 Z= 0.280 Chirality : 0.040 0.166 1783 Planarity : 0.004 0.062 2002 Dihedral : 4.409 55.927 1571 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.47 % Allowed : 18.71 % Favored : 75.82 % 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: 3.10 (0.24), residues: 1358 helix: 3.56 (0.19), residues: 720 sheet: -1.82 (0.38), residues: 134 loop : 1.01 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG n 22 TYR 0.018 0.002 TYR o 116 PHE 0.012 0.002 PHE m 109 Details of bonding type rmsd covalent geometry : bond 0.00377 (11043) covalent geometry : angle 0.56416 (14982) hydrogen bonds : bond 0.04530 ( 653) hydrogen bonds : angle 3.41501 ( 1926) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 466 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 123 LYS cc_start: 0.9111 (ttpt) cc_final: 0.8866 (tttt) REVERT: g 22 ASN cc_start: 0.8920 (m-40) cc_final: 0.8568 (m-40) REVERT: g 45 LYS cc_start: 0.8289 (ptpp) cc_final: 0.7765 (mttp) REVERT: g 123 LYS cc_start: 0.8737 (tttp) cc_final: 0.8369 (ttpp) REVERT: g 128 LYS cc_start: 0.8850 (ttpt) cc_final: 0.8463 (ttpt) REVERT: h 30 ASN cc_start: 0.9193 (m-40) cc_final: 0.8912 (m110) REVERT: h 97 ASP cc_start: 0.8519 (p0) cc_final: 0.8231 (p0) REVERT: h 116 ILE cc_start: 0.9463 (mm) cc_final: 0.9245 (mt) REVERT: j 113 GLN cc_start: 0.8330 (mt0) cc_final: 0.7897 (mt0) REVERT: l 12 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8116 (mm-40) REVERT: l 17 ASN cc_start: 0.8641 (t0) cc_final: 0.8370 (t0) REVERT: l 131 MET cc_start: 0.8960 (tpp) cc_final: 0.8550 (tpp) REVERT: m 4 ARG cc_start: 0.4698 (OUTLIER) cc_final: 0.4311 (mtt180) REVERT: m 5 LEU cc_start: 0.7223 (tp) cc_final: 0.6977 (tp) REVERT: m 14 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: m 24 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8050 (tm-30) REVERT: m 25 ILE cc_start: 0.9409 (mt) cc_final: 0.9203 (mt) REVERT: m 41 ARG cc_start: 0.9092 (mmm-85) cc_final: 0.8849 (mmm-85) REVERT: m 96 ASP cc_start: 0.8578 (p0) cc_final: 0.8309 (p0) REVERT: m 111 ASP cc_start: 0.8216 (t0) cc_final: 0.7983 (t0) REVERT: m 115 LYS cc_start: 0.9186 (mttm) cc_final: 0.8856 (mttm) REVERT: m 130 MET cc_start: 0.9135 (tpp) cc_final: 0.8737 (tpp) REVERT: m 135 GLN cc_start: 0.7868 (mp10) cc_final: 0.7339 (mp10) REVERT: o 24 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6659 (mp0) REVERT: o 102 MET cc_start: 0.7338 (tpp) cc_final: 0.7046 (tmm) REVERT: o 104 ARG cc_start: 0.8200 (ttm-80) cc_final: 0.7755 (ttm-80) REVERT: o 107 THR cc_start: 0.9176 (m) cc_final: 0.8789 (p) REVERT: o 108 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8542 (mm-40) REVERT: o 115 LYS cc_start: 0.8953 (mmmm) cc_final: 0.8430 (mtmt) REVERT: p 9 ILE cc_start: 0.7064 (mm) cc_final: 0.6851 (tt) REVERT: i 3 LEU cc_start: 0.6738 (tt) cc_final: 0.6199 (tt) REVERT: i 92 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8222 (mtpt) REVERT: i 102 MET cc_start: 0.8860 (mmm) cc_final: 0.8608 (mmm) REVERT: i 125 MET cc_start: 0.8557 (mtp) cc_final: 0.8253 (mtp) REVERT: k 24 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8187 (tm-30) REVERT: k 118 MET cc_start: 0.9035 (tmm) cc_final: 0.8797 (tmm) REVERT: k 130 MET cc_start: 0.8868 (tpp) cc_final: 0.8494 (tpp) REVERT: n 106 ARG cc_start: 0.8567 (mtm-85) cc_final: 0.8206 (mtm180) REVERT: n 131 MET cc_start: 0.8464 (tmm) cc_final: 0.8029 (tmm) REVERT: n 135 GLN cc_start: 0.7199 (mt0) cc_final: 0.6966 (mp10) outliers start: 62 outliers final: 38 residues processed: 493 average time/residue: 0.0921 time to fit residues: 63.7130 Evaluate side-chains 490 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 449 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain 6 residue 316 LEU Chi-restraints excluded: chain f residue 22 ASN Chi-restraints excluded: chain f residue 26 SER Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 124 SER Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 91 VAL Chi-restraints excluded: chain j residue 34 VAL Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 115 ASN Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain l residue 83 VAL Chi-restraints excluded: chain l residue 114 LEU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain m residue 14 GLU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 125 SER Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 118 MET Chi-restraints excluded: chain o residue 121 THR Chi-restraints excluded: chain o residue 122 VAL Chi-restraints excluded: chain p residue 98 VAL Chi-restraints excluded: chain p residue 99 VAL Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain i residue 92 LYS Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain i residue 116 ILE Chi-restraints excluded: chain i residue 122 VAL Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 111 ASP Chi-restraints excluded: chain k residue 113 SER Chi-restraints excluded: chain n residue 112 ASN Chi-restraints excluded: chain n residue 117 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 108 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 126 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 113 GLN g 115 ASN j 30 ASN j 115 ASN l 108 GLN ** l 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 23 GLN m 32 ASN m 112 ASN o 112 ASN o 126 GLN o 135 GLN ** p 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.133907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.113871 restraints weight = 18654.879| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.74 r_work: 0.3427 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11043 Z= 0.116 Angle : 0.543 8.425 14982 Z= 0.263 Chirality : 0.038 0.140 1783 Planarity : 0.003 0.032 2002 Dihedral : 4.091 55.745 1565 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.68 % Allowed : 21.01 % Favored : 74.32 % 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: 3.19 (0.24), residues: 1358 helix: 3.62 (0.19), residues: 721 sheet: -1.68 (0.39), residues: 132 loop : 1.01 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG m 41 TYR 0.014 0.001 TYR m 87 PHE 0.017 0.001 PHE m 109 Details of bonding type rmsd covalent geometry : bond 0.00249 (11043) covalent geometry : angle 0.54333 (14982) hydrogen bonds : bond 0.04143 ( 653) hydrogen bonds : angle 3.27356 ( 1926) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 474 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 45 LYS cc_start: 0.8744 (pttt) cc_final: 0.8291 (mtmm) REVERT: f 123 LYS cc_start: 0.9108 (ttpt) cc_final: 0.8856 (tttt) REVERT: g 22 ASN cc_start: 0.8884 (m-40) cc_final: 0.8505 (m-40) REVERT: g 38 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.6855 (p0) REVERT: g 45 LYS cc_start: 0.8307 (ptpp) cc_final: 0.7759 (mttp) REVERT: g 123 LYS cc_start: 0.8691 (tttp) cc_final: 0.8315 (ttpp) REVERT: g 128 LYS cc_start: 0.8837 (ttpt) cc_final: 0.8369 (ttpt) REVERT: h 30 ASN cc_start: 0.9159 (m-40) cc_final: 0.8929 (m110) REVERT: h 97 ASP cc_start: 0.8524 (p0) cc_final: 0.8228 (p0) REVERT: l 12 GLN cc_start: 0.8359 (mm-40) cc_final: 0.8132 (mm-40) REVERT: l 17 ASN cc_start: 0.8634 (t0) cc_final: 0.8357 (t0) REVERT: l 131 MET cc_start: 0.8968 (tpp) cc_final: 0.8518 (tpp) REVERT: m 4 ARG cc_start: 0.5039 (OUTLIER) cc_final: 0.4602 (mtt180) REVERT: m 12 GLN cc_start: 0.9252 (mm-40) cc_final: 0.8952 (mm110) REVERT: m 14 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: m 24 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8032 (tm-30) REVERT: m 25 ILE cc_start: 0.9404 (mt) cc_final: 0.9159 (mt) REVERT: m 96 ASP cc_start: 0.8556 (p0) cc_final: 0.8314 (p0) REVERT: m 130 MET cc_start: 0.9124 (tpp) cc_final: 0.8719 (tpp) REVERT: m 135 GLN cc_start: 0.7895 (mp10) cc_final: 0.7272 (mp10) REVERT: o 38 TYR cc_start: 0.6301 (t80) cc_final: 0.6079 (t80) REVERT: o 102 MET cc_start: 0.7336 (tpp) cc_final: 0.6962 (tmm) REVERT: o 104 ARG cc_start: 0.8162 (ttm-80) cc_final: 0.7743 (ttm-80) REVERT: o 107 THR cc_start: 0.9170 (m) cc_final: 0.8812 (p) REVERT: o 108 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8538 (mm-40) REVERT: o 112 ASN cc_start: 0.9106 (OUTLIER) cc_final: 0.8786 (t0) REVERT: o 115 LYS cc_start: 0.8928 (mmmm) cc_final: 0.8425 (mtmt) REVERT: p 93 MET cc_start: 0.8383 (mmm) cc_final: 0.8167 (mmm) REVERT: p 113 GLN cc_start: 0.8437 (mt0) cc_final: 0.8194 (mt0) REVERT: p 128 LYS cc_start: 0.9284 (mmtm) cc_final: 0.9082 (mmtm) REVERT: 8 324 ASN cc_start: 0.7960 (m-40) cc_final: 0.7599 (p0) REVERT: i 3 LEU cc_start: 0.7073 (tt) cc_final: 0.6770 (tt) REVERT: i 74 GLU cc_start: 0.8056 (pm20) cc_final: 0.7624 (pm20) REVERT: i 92 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8363 (mtpt) REVERT: i 102 MET cc_start: 0.8851 (mmm) cc_final: 0.8554 (mmm) REVERT: i 119 LEU cc_start: 0.9171 (tp) cc_final: 0.8872 (mt) REVERT: k 24 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8196 (tm-30) REVERT: k 106 ARG cc_start: 0.8501 (mtm-85) cc_final: 0.7227 (tpt170) REVERT: k 130 MET cc_start: 0.8885 (tpp) cc_final: 0.8512 (tpp) REVERT: n 14 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7364 (pm20) REVERT: n 23 GLN cc_start: 0.8847 (tp-100) cc_final: 0.8644 (tp-100) REVERT: n 41 ARG cc_start: 0.9203 (mmm-85) cc_final: 0.8703 (mmt90) REVERT: n 106 ARG cc_start: 0.8504 (mtm-85) cc_final: 0.8141 (mtm180) REVERT: n 117 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8458 (mm-40) REVERT: n 121 THR cc_start: 0.8987 (m) cc_final: 0.8686 (m) outliers start: 53 outliers final: 32 residues processed: 493 average time/residue: 0.0937 time to fit residues: 64.6753 Evaluate side-chains 494 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 455 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain 6 residue 316 LEU Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 124 SER Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain l residue 83 VAL Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain l residue 114 LEU Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain m residue 14 GLU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 125 SER Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 112 ASN Chi-restraints excluded: chain o residue 118 MET Chi-restraints excluded: chain o residue 121 THR Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain p residue 51 VAL Chi-restraints excluded: chain p residue 98 VAL Chi-restraints excluded: chain p residue 119 LEU Chi-restraints excluded: chain p residue 129 THR Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain i residue 92 LYS Chi-restraints excluded: chain i residue 93 MET Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain i residue 116 ILE Chi-restraints excluded: chain i residue 122 VAL Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 111 ASP Chi-restraints excluded: chain k residue 113 SER Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain n residue 117 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 83 optimal weight: 6.9990 chunk 119 optimal weight: 0.6980 chunk 12 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 134 optimal weight: 7.9990 chunk 56 optimal weight: 0.0070 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 104 ASN g 113 GLN g 115 ASN j 30 ASN j 115 ASN ** l 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN m 112 ASN o 126 GLN p 22 ASN ** n 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 117 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.133708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.113591 restraints weight = 18613.048| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.76 r_work: 0.3424 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11043 Z= 0.120 Angle : 0.557 10.548 14982 Z= 0.270 Chirality : 0.038 0.141 1783 Planarity : 0.003 0.029 2002 Dihedral : 4.064 55.224 1564 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.03 % Allowed : 21.27 % Favored : 73.70 % 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: 3.19 (0.24), residues: 1358 helix: 3.58 (0.19), residues: 721 sheet: -1.30 (0.42), residues: 134 loop : 0.99 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG o 19 TYR 0.011 0.001 TYR m 87 PHE 0.016 0.001 PHE m 109 Details of bonding type rmsd covalent geometry : bond 0.00267 (11043) covalent geometry : angle 0.55661 (14982) hydrogen bonds : bond 0.04040 ( 653) hydrogen bonds : angle 3.21553 ( 1926) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 471 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 45 LYS cc_start: 0.8689 (pttt) cc_final: 0.8331 (mtmm) REVERT: f 123 LYS cc_start: 0.9094 (ttpt) cc_final: 0.8859 (tttt) REVERT: g 22 ASN cc_start: 0.8912 (m-40) cc_final: 0.8545 (m-40) REVERT: g 38 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7031 (p0) REVERT: g 45 LYS cc_start: 0.8310 (ptpp) cc_final: 0.7769 (mttp) REVERT: g 123 LYS cc_start: 0.8688 (tttp) cc_final: 0.8308 (ttpp) REVERT: h 30 ASN cc_start: 0.9157 (m-40) cc_final: 0.8931 (m110) REVERT: h 69 GLU cc_start: 0.8256 (pt0) cc_final: 0.8046 (tt0) REVERT: h 75 LYS cc_start: 0.7445 (pttt) cc_final: 0.7140 (pptt) REVERT: h 97 ASP cc_start: 0.8534 (p0) cc_final: 0.8249 (p0) REVERT: j 113 GLN cc_start: 0.8263 (mt0) cc_final: 0.7795 (mt0) REVERT: l 12 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8217 (mm-40) REVERT: l 17 ASN cc_start: 0.8665 (t0) cc_final: 0.8375 (t0) REVERT: l 131 MET cc_start: 0.8916 (tpp) cc_final: 0.8478 (tpp) REVERT: m 4 ARG cc_start: 0.4955 (OUTLIER) cc_final: 0.4541 (mtt180) REVERT: m 12 GLN cc_start: 0.9264 (mm-40) cc_final: 0.9061 (mm-40) REVERT: m 14 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: m 24 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8052 (tm-30) REVERT: m 34 ASP cc_start: 0.8357 (t70) cc_final: 0.7709 (t0) REVERT: m 87 TYR cc_start: 0.8716 (m-80) cc_final: 0.8395 (m-80) REVERT: m 96 ASP cc_start: 0.8615 (p0) cc_final: 0.8392 (p0) REVERT: m 115 LYS cc_start: 0.9098 (mttm) cc_final: 0.8818 (mttm) REVERT: m 130 MET cc_start: 0.9126 (tpp) cc_final: 0.8719 (tpp) REVERT: m 135 GLN cc_start: 0.7921 (mp10) cc_final: 0.7476 (mp10) REVERT: o 102 MET cc_start: 0.7358 (tpp) cc_final: 0.7020 (tmm) REVERT: o 104 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7733 (ttm-80) REVERT: o 107 THR cc_start: 0.9187 (m) cc_final: 0.8841 (p) REVERT: o 108 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8528 (mm-40) REVERT: o 112 ASN cc_start: 0.8953 (t0) cc_final: 0.8722 (t0) REVERT: o 115 LYS cc_start: 0.8966 (mmmm) cc_final: 0.8473 (mtmt) REVERT: o 135 GLN cc_start: 0.6683 (mp10) cc_final: 0.6458 (mm-40) REVERT: p 128 LYS cc_start: 0.9278 (mmtm) cc_final: 0.9053 (mmtm) REVERT: 8 324 ASN cc_start: 0.7988 (m-40) cc_final: 0.7709 (p0) REVERT: i 3 LEU cc_start: 0.6997 (tt) cc_final: 0.6790 (tt) REVERT: i 74 GLU cc_start: 0.8078 (pm20) cc_final: 0.7669 (pm20) REVERT: i 75 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8232 (pttt) REVERT: i 92 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8254 (mtpt) REVERT: i 102 MET cc_start: 0.8856 (mmm) cc_final: 0.8540 (mmm) REVERT: i 119 LEU cc_start: 0.9198 (tp) cc_final: 0.8934 (mt) REVERT: i 125 MET cc_start: 0.8500 (mtp) cc_final: 0.8206 (mtp) REVERT: k 10 ARG cc_start: 0.7672 (ttp80) cc_final: 0.7344 (ttt90) REVERT: k 24 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8171 (tm-30) REVERT: k 113 SER cc_start: 0.9188 (OUTLIER) cc_final: 0.8966 (m) REVERT: k 130 MET cc_start: 0.8865 (tpp) cc_final: 0.8488 (tpp) REVERT: n 14 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7442 (pm20) REVERT: n 41 ARG cc_start: 0.9176 (mmm-85) cc_final: 0.8665 (mmt90) REVERT: n 106 ARG cc_start: 0.8542 (mtm-85) cc_final: 0.8189 (mtm180) REVERT: n 121 THR cc_start: 0.9000 (m) cc_final: 0.8707 (m) outliers start: 57 outliers final: 36 residues processed: 494 average time/residue: 0.0989 time to fit residues: 67.7972 Evaluate side-chains 503 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 461 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 316 LEU Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain f residue 124 SER Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain l residue 83 VAL Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain l residue 114 LEU Chi-restraints excluded: chain l residue 115 LYS Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain m residue 14 GLU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 125 SER Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 118 MET Chi-restraints excluded: chain o residue 121 THR Chi-restraints excluded: chain p residue 28 LEU Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain p residue 51 VAL Chi-restraints excluded: chain p residue 98 VAL Chi-restraints excluded: chain p residue 119 LEU Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain i residue 92 LYS Chi-restraints excluded: chain i residue 93 MET Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain i residue 116 ILE Chi-restraints excluded: chain i residue 122 VAL Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 103 ASP Chi-restraints excluded: chain k residue 111 ASP Chi-restraints excluded: chain k residue 113 SER Chi-restraints excluded: chain n residue 14 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.0000 chunk 60 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 113 GLN g 115 ASN j 30 ASN j 50 GLN l 108 GLN l 112 ASN m 32 ASN m 92 GLN m 112 ASN o 112 ASN o 126 GLN ** n 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.133385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.113278 restraints weight = 18781.322| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.75 r_work: 0.3425 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11043 Z= 0.121 Angle : 0.577 11.648 14982 Z= 0.273 Chirality : 0.038 0.141 1783 Planarity : 0.003 0.028 2002 Dihedral : 4.018 55.161 1563 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.12 % Allowed : 21.89 % Favored : 72.99 % 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: 3.18 (0.24), residues: 1358 helix: 3.55 (0.19), residues: 722 sheet: -1.28 (0.42), residues: 134 loop : 0.99 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG o 22 TYR 0.011 0.001 TYR o 116 PHE 0.016 0.002 PHE m 109 Details of bonding type rmsd covalent geometry : bond 0.00274 (11043) covalent geometry : angle 0.57728 (14982) hydrogen bonds : bond 0.04020 ( 653) hydrogen bonds : angle 3.20443 ( 1926) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 468 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 325 GLU cc_start: 0.7665 (pm20) cc_final: 0.7278 (pm20) REVERT: f 45 LYS cc_start: 0.8665 (pttt) cc_final: 0.8293 (mtmm) REVERT: f 123 LYS cc_start: 0.9070 (ttpt) cc_final: 0.8842 (tttt) REVERT: g 22 ASN cc_start: 0.8939 (m-40) cc_final: 0.8563 (m-40) REVERT: g 38 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7059 (p0) REVERT: g 45 LYS cc_start: 0.8311 (ptpp) cc_final: 0.7772 (mttp) REVERT: g 123 LYS cc_start: 0.8708 (tttp) cc_final: 0.8305 (ttpp) REVERT: g 128 LYS cc_start: 0.8851 (ttpt) cc_final: 0.8489 (ttpt) REVERT: h 30 ASN cc_start: 0.9180 (m-40) cc_final: 0.8972 (m110) REVERT: h 75 LYS cc_start: 0.7376 (pttt) cc_final: 0.7158 (pptt) REVERT: h 93 MET cc_start: 0.8736 (mmm) cc_final: 0.8428 (mmt) REVERT: h 97 ASP cc_start: 0.8558 (p0) cc_final: 0.8269 (p0) REVERT: j 113 GLN cc_start: 0.8259 (mt0) cc_final: 0.7814 (mt0) REVERT: l 12 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8240 (mm-40) REVERT: l 17 ASN cc_start: 0.8602 (t0) cc_final: 0.8315 (t0) REVERT: l 131 MET cc_start: 0.8911 (tpp) cc_final: 0.8492 (tpp) REVERT: m 4 ARG cc_start: 0.4797 (OUTLIER) cc_final: 0.4256 (mtt180) REVERT: m 14 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: m 24 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8050 (tm-30) REVERT: m 34 ASP cc_start: 0.8380 (t70) cc_final: 0.7743 (t0) REVERT: m 87 TYR cc_start: 0.8784 (m-80) cc_final: 0.8427 (m-80) REVERT: m 115 LYS cc_start: 0.9133 (mttm) cc_final: 0.8903 (mttm) REVERT: m 130 MET cc_start: 0.9117 (tpp) cc_final: 0.8701 (tpp) REVERT: m 135 GLN cc_start: 0.7948 (mp10) cc_final: 0.7485 (mp10) REVERT: o 24 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6563 (mp0) REVERT: o 102 MET cc_start: 0.7307 (tpp) cc_final: 0.7011 (tmm) REVERT: o 104 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7706 (ttm-80) REVERT: o 107 THR cc_start: 0.9206 (m) cc_final: 0.8858 (p) REVERT: o 108 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8525 (mm-40) REVERT: o 115 LYS cc_start: 0.8921 (mmmm) cc_final: 0.8521 (mtmt) REVERT: p 128 LYS cc_start: 0.9282 (mmtm) cc_final: 0.9016 (mmtm) REVERT: 8 324 ASN cc_start: 0.8099 (m-40) cc_final: 0.7839 (p0) REVERT: i 3 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6893 (tt) REVERT: i 74 GLU cc_start: 0.8118 (pm20) cc_final: 0.7763 (pm20) REVERT: i 75 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8413 (mmmt) REVERT: i 92 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8355 (mtpt) REVERT: i 102 MET cc_start: 0.8839 (mmm) cc_final: 0.8494 (mmm) REVERT: i 119 LEU cc_start: 0.9207 (tp) cc_final: 0.8950 (mt) REVERT: k 10 ARG cc_start: 0.7750 (ttp80) cc_final: 0.7401 (ttt90) REVERT: k 24 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8130 (tm-30) REVERT: k 113 SER cc_start: 0.9183 (OUTLIER) cc_final: 0.8964 (m) REVERT: k 115 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8594 (mmtp) REVERT: k 130 MET cc_start: 0.8863 (tpp) cc_final: 0.8482 (tpp) REVERT: n 14 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7517 (pm20) REVERT: n 41 ARG cc_start: 0.9151 (mmm-85) cc_final: 0.8599 (mmt90) REVERT: n 106 ARG cc_start: 0.8552 (mtm-85) cc_final: 0.8181 (mtm180) REVERT: n 121 THR cc_start: 0.9024 (m) cc_final: 0.8730 (m) outliers start: 58 outliers final: 43 residues processed: 491 average time/residue: 0.0970 time to fit residues: 66.6344 Evaluate side-chains 511 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 461 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain 6 residue 316 LEU Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain f residue 124 SER Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 14 LEU Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain l residue 83 VAL Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain l residue 114 LEU Chi-restraints excluded: chain l residue 115 LYS Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain m residue 14 GLU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 103 ASP Chi-restraints excluded: chain m residue 125 SER Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 112 ASN Chi-restraints excluded: chain o residue 118 MET Chi-restraints excluded: chain o residue 121 THR Chi-restraints excluded: chain o residue 122 VAL Chi-restraints excluded: chain p residue 28 LEU Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain p residue 51 VAL Chi-restraints excluded: chain p residue 98 VAL Chi-restraints excluded: chain p residue 99 VAL Chi-restraints excluded: chain p residue 119 LEU Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 92 LYS Chi-restraints excluded: chain i residue 93 MET Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain i residue 116 ILE Chi-restraints excluded: chain i residue 122 VAL Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 103 ASP Chi-restraints excluded: chain k residue 111 ASP Chi-restraints excluded: chain k residue 113 SER Chi-restraints excluded: chain n residue 5 LEU Chi-restraints excluded: chain n residue 14 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 113 GLN j 30 ASN m 112 ASN o 112 ASN p 115 ASN n 112 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.127295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.108022 restraints weight = 18638.889| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.64 r_work: 0.3361 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11043 Z= 0.183 Angle : 0.624 14.527 14982 Z= 0.302 Chirality : 0.040 0.148 1783 Planarity : 0.003 0.032 2002 Dihedral : 4.249 57.035 1563 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.47 % Allowed : 21.62 % Favored : 72.90 % 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: 2.88 (0.23), residues: 1358 helix: 3.27 (0.18), residues: 728 sheet: -1.38 (0.41), residues: 134 loop : 0.87 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG o 22 TYR 0.013 0.002 TYR h 112 PHE 0.016 0.002 PHE m 109 Details of bonding type rmsd covalent geometry : bond 0.00425 (11043) covalent geometry : angle 0.62414 (14982) hydrogen bonds : bond 0.04840 ( 653) hydrogen bonds : angle 3.41132 ( 1926) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 475 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 45 LYS cc_start: 0.8702 (pttt) cc_final: 0.8328 (mtmm) REVERT: f 123 LYS cc_start: 0.9117 (ttpt) cc_final: 0.8903 (tttt) REVERT: g 22 ASN cc_start: 0.8968 (m-40) cc_final: 0.8539 (m110) REVERT: g 38 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7231 (p0) REVERT: g 123 LYS cc_start: 0.8783 (tttp) cc_final: 0.8436 (ttpp) REVERT: g 128 LYS cc_start: 0.8943 (ttpt) cc_final: 0.8458 (ttpt) REVERT: h 75 LYS cc_start: 0.7508 (pttt) cc_final: 0.7268 (pptt) REVERT: h 93 MET cc_start: 0.8729 (mmm) cc_final: 0.8382 (mmt) REVERT: h 97 ASP cc_start: 0.8542 (p0) cc_final: 0.8332 (p0) REVERT: j 113 GLN cc_start: 0.8546 (mt0) cc_final: 0.8117 (mt0) REVERT: l 12 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8229 (mm110) REVERT: l 17 ASN cc_start: 0.8739 (t0) cc_final: 0.8451 (t0) REVERT: l 131 MET cc_start: 0.8912 (tpp) cc_final: 0.8516 (tpp) REVERT: m 4 ARG cc_start: 0.4952 (OUTLIER) cc_final: 0.4383 (mtt180) REVERT: m 5 LEU cc_start: 0.7249 (tp) cc_final: 0.7033 (tp) REVERT: m 14 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: m 130 MET cc_start: 0.9141 (tpp) cc_final: 0.8763 (tpp) REVERT: m 135 GLN cc_start: 0.7999 (mp10) cc_final: 0.7607 (mp10) REVERT: o 102 MET cc_start: 0.7390 (tpp) cc_final: 0.7023 (tmm) REVERT: o 108 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8605 (mm-40) REVERT: o 115 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8477 (mtmt) REVERT: p 93 MET cc_start: 0.8469 (mmm) cc_final: 0.8096 (mmt) REVERT: p 128 LYS cc_start: 0.9346 (mmtm) cc_final: 0.9105 (mmtm) REVERT: i 3 LEU cc_start: 0.7788 (tt) cc_final: 0.7525 (tt) REVERT: i 74 GLU cc_start: 0.8137 (pm20) cc_final: 0.7857 (pm20) REVERT: i 75 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8490 (mmmt) REVERT: i 92 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8375 (mtpt) REVERT: i 119 LEU cc_start: 0.9243 (tp) cc_final: 0.8989 (mt) REVERT: k 10 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7426 (tpt-90) REVERT: k 24 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8133 (tm-30) REVERT: k 115 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8489 (mmtp) REVERT: k 130 MET cc_start: 0.8887 (tpp) cc_final: 0.8586 (tpp) REVERT: n 14 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7511 (pm20) REVERT: n 106 ARG cc_start: 0.8551 (mtm-85) cc_final: 0.8217 (mtm180) outliers start: 62 outliers final: 48 residues processed: 503 average time/residue: 0.0947 time to fit residues: 66.2970 Evaluate side-chains 515 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 462 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain 6 residue 316 LEU Chi-restraints excluded: chain f residue 26 SER Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 124 SER Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 126 MET Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 14 LEU Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain l residue 83 VAL Chi-restraints excluded: chain l residue 114 LEU Chi-restraints excluded: chain l residue 115 LYS Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain m residue 14 GLU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 103 ASP Chi-restraints excluded: chain m residue 125 SER Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 118 MET Chi-restraints excluded: chain o residue 121 THR Chi-restraints excluded: chain o residue 126 GLN Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain p residue 51 VAL Chi-restraints excluded: chain p residue 98 VAL Chi-restraints excluded: chain p residue 99 VAL Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain i residue 92 LYS Chi-restraints excluded: chain i residue 93 MET Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain i residue 122 VAL Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 103 ASP Chi-restraints excluded: chain k residue 111 ASP Chi-restraints excluded: chain k residue 113 SER Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain n residue 34 ASP Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain n residue 133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 35 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 113 GLN g 115 ASN j 30 ASN k 132 ASN n 23 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.131242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.111293 restraints weight = 18514.100| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.71 r_work: 0.3388 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11043 Z= 0.125 Angle : 0.618 16.218 14982 Z= 0.292 Chirality : 0.039 0.178 1783 Planarity : 0.003 0.034 2002 Dihedral : 4.153 57.406 1563 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.50 % Allowed : 23.48 % Favored : 72.02 % 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: 3.07 (0.23), residues: 1358 helix: 3.42 (0.18), residues: 730 sheet: -1.32 (0.42), residues: 134 loop : 0.98 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG o 104 TYR 0.020 0.001 TYR l 116 PHE 0.017 0.001 PHE o 109 Details of bonding type rmsd covalent geometry : bond 0.00280 (11043) covalent geometry : angle 0.61815 (14982) hydrogen bonds : bond 0.04311 ( 653) hydrogen bonds : angle 3.27311 ( 1926) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 473 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 325 GLU cc_start: 0.7767 (pm20) cc_final: 0.7458 (pm20) REVERT: f 123 LYS cc_start: 0.9171 (ttpt) cc_final: 0.8902 (tttt) REVERT: g 22 ASN cc_start: 0.8964 (m-40) cc_final: 0.8550 (m110) REVERT: g 38 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7149 (p0) REVERT: g 123 LYS cc_start: 0.8725 (tttp) cc_final: 0.8353 (ttpp) REVERT: g 128 LYS cc_start: 0.8910 (ttpt) cc_final: 0.8436 (ttpt) REVERT: h 75 LYS cc_start: 0.7460 (pttt) cc_final: 0.7235 (pptt) REVERT: h 93 MET cc_start: 0.8792 (mmm) cc_final: 0.8465 (mmt) REVERT: h 117 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6577 (tm-30) REVERT: j 113 GLN cc_start: 0.8499 (mt0) cc_final: 0.8083 (mt0) REVERT: l 12 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8249 (mm110) REVERT: l 17 ASN cc_start: 0.8686 (t0) cc_final: 0.8395 (t0) REVERT: l 131 MET cc_start: 0.8890 (tpp) cc_final: 0.8480 (tpp) REVERT: m 4 ARG cc_start: 0.5169 (OUTLIER) cc_final: 0.4764 (mtt180) REVERT: m 14 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: m 87 TYR cc_start: 0.8737 (m-80) cc_final: 0.8475 (m-80) REVERT: m 130 MET cc_start: 0.9135 (tpp) cc_final: 0.8767 (tpp) REVERT: m 135 GLN cc_start: 0.8024 (mp10) cc_final: 0.7646 (mp10) REVERT: o 102 MET cc_start: 0.7277 (tpp) cc_final: 0.6978 (tmm) REVERT: o 104 ARG cc_start: 0.8412 (ttm-80) cc_final: 0.7795 (ttm-80) REVERT: o 107 THR cc_start: 0.9256 (m) cc_final: 0.8836 (p) REVERT: o 108 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8579 (mm-40) REVERT: o 115 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8588 (mtmt) REVERT: o 135 GLN cc_start: 0.7522 (mm-40) cc_final: 0.6989 (mp10) REVERT: p 93 MET cc_start: 0.8478 (mmm) cc_final: 0.8081 (mmt) REVERT: p 128 LYS cc_start: 0.9329 (mmtm) cc_final: 0.9036 (mmtm) REVERT: i 3 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7603 (tt) REVERT: i 74 GLU cc_start: 0.8077 (pm20) cc_final: 0.7800 (pm20) REVERT: i 75 LYS cc_start: 0.8695 (mmtt) cc_final: 0.8378 (mmmt) REVERT: i 92 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8362 (mtpt) REVERT: i 102 MET cc_start: 0.8927 (mmm) cc_final: 0.8663 (mmm) REVERT: i 119 LEU cc_start: 0.9233 (tp) cc_final: 0.8978 (mt) REVERT: k 10 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7347 (tpt-90) REVERT: k 115 LYS cc_start: 0.8896 (mmtt) cc_final: 0.8575 (mmtp) REVERT: k 130 MET cc_start: 0.8929 (tpp) cc_final: 0.8565 (tpp) REVERT: n 14 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: n 106 ARG cc_start: 0.8472 (mtm-85) cc_final: 0.8080 (mtm180) REVERT: n 121 THR cc_start: 0.9123 (m) cc_final: 0.8837 (m) outliers start: 51 outliers final: 40 residues processed: 497 average time/residue: 0.0981 time to fit residues: 67.9099 Evaluate side-chains 509 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 463 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain 6 residue 316 LEU Chi-restraints excluded: chain f residue 26 SER Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain f residue 124 SER Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 126 MET Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 14 LEU Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 122 VAL Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain l residue 83 VAL Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain l residue 114 LEU Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain m residue 14 GLU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 125 SER Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 118 MET Chi-restraints excluded: chain o residue 121 THR Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain p residue 51 VAL Chi-restraints excluded: chain p residue 98 VAL Chi-restraints excluded: chain p residue 99 VAL Chi-restraints excluded: chain p residue 119 LEU Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain i residue 92 LYS Chi-restraints excluded: chain i residue 93 MET Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain i residue 122 VAL Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 103 ASP Chi-restraints excluded: chain k residue 111 ASP Chi-restraints excluded: chain k residue 113 SER Chi-restraints excluded: chain n residue 14 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 103 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 8 optimal weight: 0.0980 chunk 48 optimal weight: 0.5980 chunk 31 optimal weight: 0.0270 chunk 87 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 113 GLN j 30 ASN l 108 GLN i 115 ASN k 132 ASN ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.132429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.112592 restraints weight = 18497.063| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.72 r_work: 0.3409 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11043 Z= 0.118 Angle : 0.616 16.673 14982 Z= 0.290 Chirality : 0.039 0.181 1783 Planarity : 0.003 0.029 2002 Dihedral : 4.072 57.049 1563 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.15 % Allowed : 24.36 % Favored : 71.49 % 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: 3.12 (0.23), residues: 1358 helix: 3.38 (0.18), residues: 732 sheet: -1.21 (0.43), residues: 125 loop : 1.05 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG o 104 TYR 0.011 0.001 TYR j 78 PHE 0.016 0.001 PHE m 109 Details of bonding type rmsd covalent geometry : bond 0.00260 (11043) covalent geometry : angle 0.61558 (14982) hydrogen bonds : bond 0.04003 ( 653) hydrogen bonds : angle 3.23498 ( 1926) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 468 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 325 GLU cc_start: 0.7813 (pm20) cc_final: 0.7505 (pm20) REVERT: f 45 LYS cc_start: 0.8761 (pttt) cc_final: 0.8132 (pttm) REVERT: f 123 LYS cc_start: 0.9171 (ttpt) cc_final: 0.8905 (tttt) REVERT: g 22 ASN cc_start: 0.8964 (m-40) cc_final: 0.8551 (m-40) REVERT: g 38 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7178 (p0) REVERT: g 123 LYS cc_start: 0.8765 (tttp) cc_final: 0.8372 (ttpp) REVERT: h 93 MET cc_start: 0.8777 (mmm) cc_final: 0.8457 (mmt) REVERT: j 82 ASN cc_start: 0.8806 (t0) cc_final: 0.8135 (t0) REVERT: l 12 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8247 (mm110) REVERT: l 17 ASN cc_start: 0.8626 (t0) cc_final: 0.8308 (t0) REVERT: l 131 MET cc_start: 0.8902 (tpp) cc_final: 0.8472 (tpp) REVERT: m 4 ARG cc_start: 0.5020 (OUTLIER) cc_final: 0.4491 (mtt-85) REVERT: m 14 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: m 130 MET cc_start: 0.9100 (tpp) cc_final: 0.8710 (tpp) REVERT: m 135 GLN cc_start: 0.8016 (mp10) cc_final: 0.7619 (mp10) REVERT: o 102 MET cc_start: 0.7344 (tpp) cc_final: 0.7044 (tmm) REVERT: o 104 ARG cc_start: 0.8393 (ttm-80) cc_final: 0.7811 (ttm-80) REVERT: o 107 THR cc_start: 0.9261 (m) cc_final: 0.8933 (p) REVERT: o 108 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8553 (mm-40) REVERT: o 115 LYS cc_start: 0.8941 (mmmm) cc_final: 0.8456 (mtmt) REVERT: o 132 ASN cc_start: 0.8700 (t0) cc_final: 0.8367 (t0) REVERT: o 135 GLN cc_start: 0.7585 (mm-40) cc_final: 0.7212 (mp10) REVERT: p 93 MET cc_start: 0.8463 (mmm) cc_final: 0.8115 (mmt) REVERT: p 123 LYS cc_start: 0.8169 (tptm) cc_final: 0.7622 (tptm) REVERT: p 128 LYS cc_start: 0.9264 (mmtm) cc_final: 0.8950 (mmtm) REVERT: i 74 GLU cc_start: 0.8039 (pm20) cc_final: 0.7797 (pm20) REVERT: i 75 LYS cc_start: 0.8661 (mmtt) cc_final: 0.8331 (mmmt) REVERT: i 92 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8316 (mtpt) REVERT: i 102 MET cc_start: 0.8900 (mmm) cc_final: 0.8670 (mmm) REVERT: i 119 LEU cc_start: 0.9230 (tp) cc_final: 0.8987 (mt) REVERT: k 10 ARG cc_start: 0.7805 (ttp80) cc_final: 0.7273 (tpt-90) REVERT: k 24 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7971 (tm-30) REVERT: k 113 SER cc_start: 0.9197 (OUTLIER) cc_final: 0.8931 (m) REVERT: k 115 LYS cc_start: 0.8917 (mmtt) cc_final: 0.8581 (mmtp) REVERT: k 130 MET cc_start: 0.8921 (tpp) cc_final: 0.8535 (tpp) REVERT: n 14 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: n 106 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.8120 (mtm180) REVERT: n 121 THR cc_start: 0.9123 (m) cc_final: 0.8831 (m) outliers start: 47 outliers final: 34 residues processed: 490 average time/residue: 0.0964 time to fit residues: 66.3431 Evaluate side-chains 496 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 456 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain 6 residue 316 LEU Chi-restraints excluded: chain f residue 26 SER Chi-restraints excluded: chain f residue 76 LEU Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 126 MET Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 126 MET Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain l residue 83 VAL Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain m residue 14 GLU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 103 ASP Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 121 THR Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain p residue 98 VAL Chi-restraints excluded: chain p residue 99 VAL Chi-restraints excluded: chain p residue 119 LEU Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain i residue 92 LYS Chi-restraints excluded: chain i residue 93 MET Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain i residue 122 VAL Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 103 ASP Chi-restraints excluded: chain k residue 111 ASP Chi-restraints excluded: chain k residue 113 SER Chi-restraints excluded: chain n residue 14 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 102 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 18 optimal weight: 0.0370 chunk 134 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 105 optimal weight: 0.2980 chunk 77 optimal weight: 0.0070 chunk 30 optimal weight: 0.7980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 115 ASN j 30 ASN m 32 ASN i 88 ASN i 115 ASN k 132 ASN ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.133492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.113766 restraints weight = 18602.460| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.70 r_work: 0.3424 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11043 Z= 0.118 Angle : 0.646 16.531 14982 Z= 0.301 Chirality : 0.039 0.172 1783 Planarity : 0.003 0.028 2002 Dihedral : 4.069 57.213 1563 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.44 % Allowed : 25.24 % Favored : 71.32 % 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: 3.08 (0.24), residues: 1358 helix: 3.32 (0.18), residues: 732 sheet: -1.10 (0.39), residues: 142 loop : 1.14 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG o 104 TYR 0.012 0.001 TYR l 116 PHE 0.017 0.001 PHE m 109 Details of bonding type rmsd covalent geometry : bond 0.00260 (11043) covalent geometry : angle 0.64623 (14982) hydrogen bonds : bond 0.03847 ( 653) hydrogen bonds : angle 3.23944 ( 1926) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 465 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 325 GLU cc_start: 0.7819 (pm20) cc_final: 0.7515 (pm20) REVERT: f 45 LYS cc_start: 0.8763 (pttt) cc_final: 0.8138 (pttm) REVERT: f 123 LYS cc_start: 0.9132 (ttpt) cc_final: 0.8874 (tttt) REVERT: g 22 ASN cc_start: 0.8935 (m-40) cc_final: 0.8531 (m-40) REVERT: g 38 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7068 (p0) REVERT: g 123 LYS cc_start: 0.8769 (tttp) cc_final: 0.8388 (ttpp) REVERT: g 128 LYS cc_start: 0.8867 (ttmt) cc_final: 0.8603 (ttpt) REVERT: h 78 TYR cc_start: 0.9049 (t80) cc_final: 0.8564 (t80) REVERT: j 82 ASN cc_start: 0.8793 (t0) cc_final: 0.8104 (t0) REVERT: j 88 ASN cc_start: 0.8636 (m110) cc_final: 0.8343 (m-40) REVERT: j 113 GLN cc_start: 0.8221 (mt0) cc_final: 0.7755 (mt0) REVERT: j 128 LYS cc_start: 0.8843 (mtpt) cc_final: 0.8559 (ttpt) REVERT: l 17 ASN cc_start: 0.8642 (t0) cc_final: 0.8346 (t0) REVERT: l 131 MET cc_start: 0.8882 (tpp) cc_final: 0.8467 (tpp) REVERT: m 4 ARG cc_start: 0.5098 (OUTLIER) cc_final: 0.4332 (mtt-85) REVERT: m 14 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: m 130 MET cc_start: 0.9060 (tpp) cc_final: 0.8647 (tpp) REVERT: m 135 GLN cc_start: 0.8029 (mp10) cc_final: 0.7638 (mp10) REVERT: o 102 MET cc_start: 0.7327 (tpp) cc_final: 0.7043 (tmm) REVERT: o 104 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.7796 (ttm-80) REVERT: o 107 THR cc_start: 0.9253 (m) cc_final: 0.8945 (p) REVERT: o 108 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8551 (mm-40) REVERT: o 115 LYS cc_start: 0.8930 (mmmm) cc_final: 0.8452 (mtmt) REVERT: o 132 ASN cc_start: 0.8726 (t0) cc_final: 0.8407 (t0) REVERT: o 135 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7239 (mp10) REVERT: p 93 MET cc_start: 0.8482 (mmm) cc_final: 0.8137 (mmt) REVERT: p 128 LYS cc_start: 0.9215 (mmtm) cc_final: 0.8905 (mmtm) REVERT: 8 324 ASN cc_start: 0.8184 (m-40) cc_final: 0.7750 (m110) REVERT: i 74 GLU cc_start: 0.8023 (pm20) cc_final: 0.7760 (pm20) REVERT: i 75 LYS cc_start: 0.8654 (mmtt) cc_final: 0.8338 (mmmt) REVERT: i 92 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8271 (mtpt) REVERT: i 102 MET cc_start: 0.8864 (mmm) cc_final: 0.8651 (mmm) REVERT: i 119 LEU cc_start: 0.9230 (tp) cc_final: 0.9021 (mt) REVERT: k 10 ARG cc_start: 0.7760 (ttp80) cc_final: 0.7172 (tpt-90) REVERT: k 24 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7961 (tm-30) REVERT: k 113 SER cc_start: 0.9135 (OUTLIER) cc_final: 0.8876 (m) REVERT: k 115 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8552 (mmtp) REVERT: k 130 MET cc_start: 0.8867 (tpp) cc_final: 0.8509 (tpp) REVERT: n 14 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7539 (pm20) REVERT: n 106 ARG cc_start: 0.8426 (mtm-85) cc_final: 0.8106 (mtm180) REVERT: n 121 THR cc_start: 0.9128 (m) cc_final: 0.8831 (m) outliers start: 39 outliers final: 33 residues processed: 483 average time/residue: 0.0951 time to fit residues: 63.9261 Evaluate side-chains 489 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 450 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain 6 residue 316 LEU Chi-restraints excluded: chain f residue 76 LEU Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain g residue 38 ASP Chi-restraints excluded: chain g residue 126 MET Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 126 MET Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain l residue 83 VAL Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain m residue 14 GLU Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 103 ASP Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 121 THR Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain p residue 98 VAL Chi-restraints excluded: chain p residue 99 VAL Chi-restraints excluded: chain p residue 119 LEU Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain i residue 88 ASN Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain i residue 92 LYS Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 103 ASP Chi-restraints excluded: chain k residue 111 ASP Chi-restraints excluded: chain k residue 113 SER Chi-restraints excluded: chain n residue 14 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 113 GLN j 30 ASN l 12 GLN o 117 GLN o 126 GLN k 132 ASN ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 112 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.131734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.111895 restraints weight = 18660.269| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.73 r_work: 0.3395 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11043 Z= 0.134 Angle : 0.645 16.281 14982 Z= 0.303 Chirality : 0.039 0.165 1783 Planarity : 0.003 0.038 2002 Dihedral : 4.114 57.397 1563 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.88 % Allowed : 24.80 % Favored : 71.32 % 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: 3.12 (0.23), residues: 1358 helix: 3.34 (0.18), residues: 729 sheet: -1.31 (0.46), residues: 103 loop : 1.04 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG m 22 TYR 0.018 0.001 TYR m 87 PHE 0.020 0.002 PHE m 109 Details of bonding type rmsd covalent geometry : bond 0.00308 (11043) covalent geometry : angle 0.64459 (14982) hydrogen bonds : bond 0.04047 ( 653) hydrogen bonds : angle 3.28060 ( 1926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2625.95 seconds wall clock time: 45 minutes 40.72 seconds (2740.72 seconds total)