Starting phenix.real_space_refine on Tue Jul 29 02:29:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cg0_30348/07_2025/7cg0_30348.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cg0_30348/07_2025/7cg0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7cg0_30348/07_2025/7cg0_30348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cg0_30348/07_2025/7cg0_30348.map" model { file = "/net/cci-nas-00/data/ceres_data/7cg0_30348/07_2025/7cg0_30348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cg0_30348/07_2025/7cg0_30348.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.40, per 1000 atoms: 0.86 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: 2.63 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.93 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: 2.77 Time building geometry restraints manager: 3.14 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: 11.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.450 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.160 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 PHE 0.013 0.001 PHE o 11 TYR 0.014 0.001 TYR j 112 ARG 0.003 0.000 ARG k 106 Details of bonding type rmsd hydrogen bonds : bond 0.06647 ( 653) hydrogen bonds : angle 3.52286 ( 1926) covalent geometry : bond 0.00337 (11043) covalent geometry : angle 0.53121 (14982) *********************** 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 : 1.103 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: 0.7684 (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: 0.2446 time to fit residues: 193.1904 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 : 1.304 ------------------------------------------------------------------------------- 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 116 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 324 ASN f 30 ASN f 88 ASN g 27 ASN g 104 ASN g 113 GLN j 30 ASN j 115 ASN l 21 GLN m 32 ASN ** p 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 30 ASN p 104 ASN k 32 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.131144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.111160 restraints weight = 18294.232| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.69 r_work: 0.3412 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11043 Z= 0.213 Angle : 0.628 7.244 14982 Z= 0.320 Chirality : 0.042 0.178 1783 Planarity : 0.004 0.043 2002 Dihedral : 4.793 57.227 1574 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.21 % Allowed : 17.48 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.23), residues: 1358 helix: 3.49 (0.18), residues: 716 sheet: -1.84 (0.38), residues: 134 loop : 0.95 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE o 45 TYR 0.020 0.002 TYR g 78 ARG 0.010 0.001 ARG f 43 Details of bonding type rmsd hydrogen bonds : bond 0.04962 ( 653) hydrogen bonds : angle 3.56770 ( 1926) covalent geometry : bond 0.00481 (11043) covalent geometry : angle 0.62822 (14982) *********************** 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 530 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 471 time to evaluate : 1.280 Fit side-chains revert: symmetry clash REVERT: f 123 LYS cc_start: 0.9140 (ttpt) cc_final: 0.8907 (tttt) REVERT: g 22 ASN cc_start: 0.8907 (m-40) cc_final: 0.8585 (m-40) REVERT: g 123 LYS cc_start: 0.8826 (tttp) cc_final: 0.8485 (ttpp) REVERT: h 19 LYS cc_start: 0.9027 (mttp) cc_final: 0.8792 (mttp) REVERT: h 30 ASN cc_start: 0.9263 (m-40) cc_final: 0.9021 (m110) REVERT: h 97 ASP cc_start: 0.8404 (p0) cc_final: 0.8182 (p0) REVERT: h 102 MET cc_start: 0.8737 (mmm) cc_final: 0.8403 (mmt) REVERT: j 113 GLN cc_start: 0.8409 (mt0) cc_final: 0.8108 (mt0) REVERT: l 12 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8117 (mm-40) REVERT: l 17 ASN cc_start: 0.8726 (t0) cc_final: 0.8452 (t0) REVERT: l 26 LEU cc_start: 0.9062 (mt) cc_final: 0.8846 (mm) REVERT: l 131 MET cc_start: 0.8935 (tpp) cc_final: 0.8543 (tpp) REVERT: m 4 ARG cc_start: 0.4901 (OUTLIER) cc_final: 0.4442 (mtt180) REVERT: m 5 LEU cc_start: 0.7509 (tp) cc_final: 0.7256 (tp) REVERT: m 14 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: m 23 GLN cc_start: 0.8968 (tp-100) cc_final: 0.8725 (tp40) REVERT: m 41 ARG cc_start: 0.9123 (mmm-85) cc_final: 0.8878 (mmm-85) REVERT: m 96 ASP cc_start: 0.8562 (p0) cc_final: 0.8347 (p0) REVERT: m 130 MET cc_start: 0.9081 (tpp) cc_final: 0.8773 (tpp) REVERT: m 135 GLN cc_start: 0.7942 (mp10) cc_final: 0.7457 (mp10) REVERT: o 24 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6854 (mt-10) REVERT: o 102 MET cc_start: 0.7424 (tpp) cc_final: 0.7086 (tmm) REVERT: o 108 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8622 (mm-40) REVERT: o 115 LYS cc_start: 0.8925 (mmmm) cc_final: 0.8184 (mtmt) REVERT: o 132 ASN cc_start: 0.8546 (t0) cc_final: 0.8317 (t0) REVERT: p 9 ILE cc_start: 0.7057 (mm) cc_final: 0.6832 (tt) REVERT: p 43 ARG cc_start: 0.6649 (ttt180) cc_final: 0.6420 (mtt180) REVERT: i 74 GLU cc_start: 0.8149 (pm20) cc_final: 0.7920 (pm20) REVERT: i 92 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8199 (mtpt) REVERT: i 102 MET cc_start: 0.8836 (mmm) cc_final: 0.8581 (mmm) REVERT: k 24 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8232 (tm-30) REVERT: k 118 MET cc_start: 0.9016 (tmm) cc_final: 0.8779 (tmm) REVERT: k 130 MET cc_start: 0.8840 (tpp) cc_final: 0.8495 (tpp) REVERT: n 106 ARG cc_start: 0.8589 (mtm-85) cc_final: 0.8230 (mtm180) REVERT: n 112 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8869 (t0) REVERT: n 121 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8830 (m) outliers start: 59 outliers final: 34 residues processed: 503 average time/residue: 0.2631 time to fit residues: 183.1485 Evaluate side-chains 490 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 450 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain f residue 26 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 14 LEU Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 91 VAL Chi-restraints excluded: chain h residue 122 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 54 VAL 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 125 SER Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain o residue 24 GLU Chi-restraints excluded: chain o residue 83 VAL Chi-restraints excluded: chain o residue 118 MET Chi-restraints excluded: chain o residue 122 VAL Chi-restraints excluded: chain p residue 98 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 121 THR 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 Chi-restraints excluded: chain n residue 121 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 10 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 53 optimal weight: 0.0010 chunk 43 optimal weight: 0.0870 chunk 49 optimal weight: 0.7980 overall best weight: 0.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 22 ASN f 46 GLN 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 32 ASN m 92 GLN o 126 GLN o 135 GLN ** p 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 23 GLN n 112 ASN ** n 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.133380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.113318 restraints weight = 18699.208| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.73 r_work: 0.3415 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11043 Z= 0.115 Angle : 0.546 8.711 14982 Z= 0.266 Chirality : 0.038 0.161 1783 Planarity : 0.003 0.035 2002 Dihedral : 4.121 56.257 1565 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.06 % Allowed : 20.74 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.24), residues: 1358 helix: 3.70 (0.19), residues: 718 sheet: -1.44 (0.37), residues: 154 loop : 1.00 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE o 11 TYR 0.014 0.001 TYR o 116 ARG 0.003 0.000 ARG l 10 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 653) hydrogen bonds : angle 3.30464 ( 1926) covalent geometry : bond 0.00244 (11043) covalent geometry : angle 0.54566 (14982) *********************** 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 519 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 473 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 45 LYS cc_start: 0.8727 (pttt) cc_final: 0.8375 (mtmm) REVERT: f 69 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7749 (mm-30) REVERT: f 102 MET cc_start: 0.8806 (mmm) cc_final: 0.8550 (mmm) REVERT: f 123 LYS cc_start: 0.9100 (ttpt) cc_final: 0.8834 (tttt) REVERT: g 22 ASN cc_start: 0.8883 (m-40) cc_final: 0.8514 (m-40) REVERT: g 123 LYS cc_start: 0.8795 (tttp) cc_final: 0.8421 (ttpp) REVERT: h 30 ASN cc_start: 0.9185 (m-40) cc_final: 0.8959 (m110) REVERT: h 75 LYS cc_start: 0.7400 (pttt) cc_final: 0.7106 (pptt) REVERT: h 102 MET cc_start: 0.8787 (mmm) cc_final: 0.8455 (mmt) REVERT: h 116 ILE cc_start: 0.9322 (mm) cc_final: 0.9095 (mt) REVERT: l 12 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8150 (mm-40) REVERT: l 17 ASN cc_start: 0.8649 (t0) cc_final: 0.8383 (t0) REVERT: l 131 MET cc_start: 0.8880 (tpp) cc_final: 0.8477 (tpp) REVERT: m 4 ARG cc_start: 0.5029 (OUTLIER) cc_final: 0.4650 (mtt180) REVERT: m 14 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: m 23 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8167 (tp40) REVERT: m 24 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7992 (tm-30) REVERT: m 87 TYR cc_start: 0.8718 (m-80) cc_final: 0.8422 (m-10) REVERT: m 96 ASP cc_start: 0.8548 (p0) cc_final: 0.8279 (p0) REVERT: m 130 MET cc_start: 0.9081 (tpp) cc_final: 0.8702 (tpp) REVERT: m 135 GLN cc_start: 0.7908 (mp10) cc_final: 0.7437 (mp10) REVERT: o 25 ILE cc_start: 0.7779 (mt) cc_final: 0.7535 (mm) REVERT: o 102 MET cc_start: 0.7387 (tpp) cc_final: 0.7003 (tmm) REVERT: o 107 THR cc_start: 0.9200 (m) cc_final: 0.8829 (p) REVERT: o 108 GLN cc_start: 0.8936 (mm-40) cc_final: 0.8565 (mm-40) REVERT: o 115 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8455 (mtmt) REVERT: 8 324 ASN cc_start: 0.7985 (m-40) cc_final: 0.7606 (p0) REVERT: i 102 MET cc_start: 0.8729 (mmm) cc_final: 0.8510 (mmm) REVERT: k 24 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8191 (tm-30) REVERT: k 130 MET cc_start: 0.8871 (tpp) cc_final: 0.8519 (tpp) REVERT: n 106 ARG cc_start: 0.8506 (mtm-85) cc_final: 0.8152 (mtm180) REVERT: n 121 THR cc_start: 0.9047 (m) cc_final: 0.8744 (m) outliers start: 46 outliers final: 28 residues processed: 491 average time/residue: 0.2308 time to fit residues: 156.1744 Evaluate side-chains 484 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 454 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 48 VAL Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 124 SER Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain j residue 34 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 30 ILE Chi-restraints excluded: chain m residue 125 SER Chi-restraints excluded: chain o residue 18 LEU Chi-restraints excluded: chain p residue 48 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 99 VAL Chi-restraints excluded: chain i residue 116 ILE 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 34 ASP Chi-restraints excluded: chain n residue 117 GLN Chi-restraints excluded: chain n residue 120 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 71 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 53 optimal weight: 0.0370 chunk 87 optimal weight: 6.9990 chunk 44 optimal weight: 0.0970 chunk 127 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.0260 ------------------------------------------------------------------------------- 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 32 ASN ** o 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 126 GLN ** p 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 115 ASN ** n 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.132343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.112230 restraints weight = 18519.305| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.72 r_work: 0.3413 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11043 Z= 0.132 Angle : 0.548 8.068 14982 Z= 0.269 Chirality : 0.038 0.159 1783 Planarity : 0.003 0.032 2002 Dihedral : 4.108 57.217 1564 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.32 % Allowed : 21.89 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.23), residues: 1358 helix: 3.56 (0.18), residues: 720 sheet: -1.42 (0.40), residues: 134 loop : 0.98 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE o 109 TYR 0.011 0.001 TYR j 112 ARG 0.004 0.000 ARG o 22 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 653) hydrogen bonds : angle 3.31209 ( 1926) covalent geometry : bond 0.00298 (11043) covalent geometry : angle 0.54843 (14982) *********************** 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 522 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 473 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 45 LYS cc_start: 0.8667 (pttt) cc_final: 0.8248 (mtmm) REVERT: f 102 MET cc_start: 0.8801 (mmm) cc_final: 0.8572 (mmm) REVERT: g 22 ASN cc_start: 0.8928 (m-40) cc_final: 0.8551 (m-40) REVERT: g 45 LYS cc_start: 0.8322 (ptpp) cc_final: 0.7779 (mttp) REVERT: g 123 LYS cc_start: 0.8792 (tttp) cc_final: 0.8409 (ttpp) REVERT: g 126 MET cc_start: 0.8391 (mmm) cc_final: 0.8012 (mtt) REVERT: g 128 LYS cc_start: 0.8870 (ttpt) cc_final: 0.8509 (ttpt) REVERT: h 69 GLU cc_start: 0.8294 (pt0) cc_final: 0.8034 (tt0) REVERT: h 75 LYS cc_start: 0.7472 (pttt) cc_final: 0.7099 (pptt) REVERT: h 102 MET cc_start: 0.8715 (mmm) cc_final: 0.8394 (mmt) REVERT: h 116 ILE cc_start: 0.9354 (mm) cc_final: 0.9141 (mt) REVERT: j 113 GLN cc_start: 0.8412 (mt0) cc_final: 0.7977 (mt0) REVERT: j 126 MET cc_start: 0.9332 (mmm) cc_final: 0.8949 (mtt) REVERT: l 12 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8197 (mm-40) REVERT: l 17 ASN cc_start: 0.8596 (t0) cc_final: 0.8328 (t0) REVERT: l 131 MET cc_start: 0.8892 (tpp) cc_final: 0.8490 (tpp) REVERT: m 4 ARG cc_start: 0.5105 (OUTLIER) cc_final: 0.4680 (mtt180) REVERT: m 14 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: m 23 GLN cc_start: 0.8949 (tp-100) cc_final: 0.8113 (tp40) REVERT: m 24 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8014 (tm-30) REVERT: m 54 VAL cc_start: 0.6811 (t) cc_final: 0.6604 (m) REVERT: m 87 TYR cc_start: 0.8758 (m-80) cc_final: 0.8525 (m-80) REVERT: m 96 ASP cc_start: 0.8596 (p0) cc_final: 0.8365 (p0) REVERT: m 130 MET cc_start: 0.9135 (tpp) cc_final: 0.8704 (tpp) REVERT: m 135 GLN cc_start: 0.7950 (mp10) cc_final: 0.7321 (mp10) REVERT: o 25 ILE cc_start: 0.7654 (mt) cc_final: 0.7439 (mm) REVERT: o 107 THR cc_start: 0.9199 (m) cc_final: 0.8817 (p) REVERT: o 108 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8613 (mm-40) REVERT: o 115 LYS cc_start: 0.8886 (mmmm) cc_final: 0.8294 (mtmt) REVERT: i 74 GLU cc_start: 0.8151 (pm20) cc_final: 0.7891 (pm20) REVERT: i 75 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8207 (pttt) REVERT: i 92 LYS cc_start: 0.8697 (mtpt) cc_final: 0.8356 (mtpt) REVERT: i 119 LEU cc_start: 0.9192 (tp) cc_final: 0.8912 (mt) REVERT: k 24 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8174 (tm-30) REVERT: k 130 MET cc_start: 0.8895 (tpp) cc_final: 0.8545 (tpp) REVERT: n 14 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7116 (pm20) REVERT: n 41 ARG cc_start: 0.9206 (mmm-85) cc_final: 0.8623 (mmt90) REVERT: n 106 ARG cc_start: 0.8537 (mtm-85) cc_final: 0.8188 (mtm180) REVERT: n 117 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8522 (mm-40) REVERT: n 121 THR cc_start: 0.9063 (m) cc_final: 0.8777 (m) outliers start: 49 outliers final: 35 residues processed: 495 average time/residue: 0.2264 time to fit residues: 154.9343 Evaluate side-chains 495 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 456 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 48 VAL 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 18 SER Chi-restraints excluded: chain h residue 14 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 54 VAL 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 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 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 119 LEU Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain i residue 93 MET 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 Chi-restraints excluded: chain n residue 117 GLN Chi-restraints excluded: chain n residue 120 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 80 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 46 GLN f 104 ASN g 113 GLN g 115 ASN j 30 ASN l 23 GLN l 108 GLN l 112 ASN m 32 ASN p 22 ASN p 120 ASN n 23 GLN ** n 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.130143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.110515 restraints weight = 18540.506| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.67 r_work: 0.3380 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4007 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= 0.154 Angle : 0.575 11.205 14982 Z= 0.282 Chirality : 0.039 0.154 1783 Planarity : 0.003 0.039 2002 Dihedral : 4.168 57.640 1564 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.56 % Allowed : 21.71 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.23), residues: 1358 helix: 3.45 (0.18), residues: 721 sheet: -1.47 (0.41), residues: 134 loop : 0.92 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE o 109 TYR 0.014 0.001 TYR l 87 ARG 0.006 0.000 ARG l 41 Details of bonding type rmsd hydrogen bonds : bond 0.04517 ( 653) hydrogen bonds : angle 3.32980 ( 1926) covalent geometry : bond 0.00348 (11043) covalent geometry : angle 0.57509 (14982) *********************** 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 540 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 477 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 45 LYS cc_start: 0.8702 (pttt) cc_final: 0.8260 (mtmm) REVERT: f 102 MET cc_start: 0.8827 (mmm) cc_final: 0.8588 (mmm) REVERT: g 22 ASN cc_start: 0.8972 (m-40) cc_final: 0.8566 (m110) REVERT: g 123 LYS cc_start: 0.8778 (tttp) cc_final: 0.8397 (ttpp) REVERT: g 126 MET cc_start: 0.8549 (mmm) cc_final: 0.8180 (mtt) REVERT: g 128 LYS cc_start: 0.8921 (ttpt) cc_final: 0.8481 (ttpt) REVERT: h 75 LYS cc_start: 0.7470 (pttt) cc_final: 0.7184 (pptt) REVERT: h 102 MET cc_start: 0.8735 (mmm) cc_final: 0.8397 (mmt) REVERT: j 113 GLN cc_start: 0.8461 (mt0) cc_final: 0.8014 (mt0) REVERT: l 12 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8229 (mm110) REVERT: l 17 ASN cc_start: 0.8672 (t0) cc_final: 0.8388 (t0) REVERT: l 131 MET cc_start: 0.8932 (tpp) cc_final: 0.8521 (tpp) REVERT: m 4 ARG cc_start: 0.4989 (OUTLIER) cc_final: 0.4556 (mtt180) REVERT: m 5 LEU cc_start: 0.7189 (tp) cc_final: 0.6983 (tp) REVERT: m 14 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: m 23 GLN cc_start: 0.8957 (tp-100) cc_final: 0.8134 (tp40) REVERT: m 87 TYR cc_start: 0.8830 (m-80) cc_final: 0.8591 (m-80) REVERT: m 96 ASP cc_start: 0.8680 (p0) cc_final: 0.8474 (p0) REVERT: m 115 LYS cc_start: 0.9153 (mttm) cc_final: 0.8915 (mttm) REVERT: m 130 MET cc_start: 0.9134 (tpp) cc_final: 0.8719 (tpp) REVERT: m 135 GLN cc_start: 0.7974 (mp10) cc_final: 0.7285 (mp10) REVERT: o 102 MET cc_start: 0.7613 (mmp) cc_final: 0.7122 (tmm) REVERT: o 107 THR cc_start: 0.9209 (m) cc_final: 0.8785 (p) REVERT: o 108 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8613 (mm-40) REVERT: o 115 LYS cc_start: 0.8971 (mmmm) cc_final: 0.8401 (mtmt) REVERT: o 127 LEU cc_start: 0.7946 (tt) cc_final: 0.7677 (tp) REVERT: o 135 GLN cc_start: 0.7582 (mm-40) cc_final: 0.6933 (mp10) REVERT: 8 324 ASN cc_start: 0.8152 (m-40) cc_final: 0.7769 (p0) REVERT: i 74 GLU cc_start: 0.8106 (pm20) cc_final: 0.7770 (pm20) REVERT: i 75 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8439 (mmmt) REVERT: i 92 LYS cc_start: 0.8725 (mtpt) cc_final: 0.8320 (mtpt) REVERT: i 119 LEU cc_start: 0.9202 (tp) cc_final: 0.8949 (mt) REVERT: k 10 ARG cc_start: 0.7807 (ttp80) cc_final: 0.7470 (ttt90) REVERT: k 24 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8139 (tm-30) REVERT: k 130 MET cc_start: 0.8934 (tpp) cc_final: 0.8576 (tpp) REVERT: n 106 ARG cc_start: 0.8554 (mtm-85) cc_final: 0.8261 (mtm180) REVERT: n 117 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8653 (mm-40) REVERT: n 121 THR cc_start: 0.9116 (m) cc_final: 0.8846 (m) outliers start: 63 outliers final: 50 residues processed: 501 average time/residue: 0.2409 time to fit residues: 167.0064 Evaluate side-chains 517 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 464 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain 6 residue 316 LEU Chi-restraints excluded: chain 7 residue 319 GLN Chi-restraints excluded: chain f residue 48 VAL Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 107 SER Chi-restraints excluded: chain f residue 124 SER Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain g residue 3 LEU 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 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 24 GLU Chi-restraints excluded: chain l residue 83 VAL Chi-restraints excluded: chain l residue 84 ASP 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 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 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 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 34 ASP Chi-restraints excluded: chain n residue 117 GLN Chi-restraints excluded: chain n residue 133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 m 32 ASN m 92 GLN p 22 ASN k 132 ASN ** n 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.130029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.110193 restraints weight = 18646.897| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.72 r_work: 0.3392 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11043 Z= 0.134 Angle : 0.579 11.432 14982 Z= 0.281 Chirality : 0.039 0.165 1783 Planarity : 0.003 0.036 2002 Dihedral : 4.145 58.311 1564 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.77 % Allowed : 23.39 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.23), residues: 1358 helix: 3.43 (0.19), residues: 728 sheet: -1.48 (0.41), residues: 134 loop : 0.92 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE o 11 TYR 0.011 0.001 TYR j 78 ARG 0.004 0.000 ARG j 43 Details of bonding type rmsd hydrogen bonds : bond 0.04404 ( 653) hydrogen bonds : angle 3.31074 ( 1926) covalent geometry : bond 0.00302 (11043) covalent geometry : angle 0.57917 (14982) *********************** 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 529 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 475 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 102 MET cc_start: 0.8792 (mmm) cc_final: 0.8556 (mmm) REVERT: g 22 ASN cc_start: 0.8950 (m-40) cc_final: 0.8555 (m110) REVERT: g 123 LYS cc_start: 0.8777 (tttp) cc_final: 0.8412 (ttpp) REVERT: g 126 MET cc_start: 0.8577 (mmm) cc_final: 0.8301 (mtt) REVERT: g 128 LYS cc_start: 0.8915 (ttpt) cc_final: 0.8450 (ttpt) REVERT: h 75 LYS cc_start: 0.7449 (pttt) cc_final: 0.7199 (pptt) REVERT: h 102 MET cc_start: 0.8696 (mmm) cc_final: 0.8374 (mmt) REVERT: h 116 ILE cc_start: 0.9361 (mm) cc_final: 0.9150 (mt) REVERT: j 113 GLN cc_start: 0.8514 (mt0) cc_final: 0.8088 (mt0) REVERT: l 12 GLN cc_start: 0.8400 (mm-40) cc_final: 0.8178 (mm110) REVERT: l 17 ASN cc_start: 0.8656 (t0) cc_final: 0.8380 (t0) REVERT: l 131 MET cc_start: 0.8895 (tpp) cc_final: 0.8498 (tpp) REVERT: m 4 ARG cc_start: 0.5326 (OUTLIER) cc_final: 0.4867 (mtt180) REVERT: m 5 LEU cc_start: 0.7178 (tp) cc_final: 0.6925 (tp) REVERT: m 14 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: m 23 GLN cc_start: 0.8915 (tp-100) cc_final: 0.8115 (tp40) REVERT: m 24 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8047 (tm-30) REVERT: m 87 TYR cc_start: 0.8839 (m-80) cc_final: 0.8618 (m-80) REVERT: m 96 ASP cc_start: 0.8618 (p0) cc_final: 0.8405 (p0) REVERT: m 115 LYS cc_start: 0.9130 (mttm) cc_final: 0.8800 (mttp) REVERT: m 130 MET cc_start: 0.9128 (tpp) cc_final: 0.8726 (tpp) REVERT: m 135 GLN cc_start: 0.7981 (mp10) cc_final: 0.7302 (mp10) REVERT: o 102 MET cc_start: 0.7594 (mmp) cc_final: 0.7213 (tmm) REVERT: o 107 THR cc_start: 0.9247 (m) cc_final: 0.8880 (p) REVERT: o 108 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8684 (mm-40) REVERT: o 115 LYS cc_start: 0.8976 (mmmm) cc_final: 0.8515 (mtmt) REVERT: o 132 ASN cc_start: 0.8610 (t0) cc_final: 0.8362 (t0) REVERT: o 135 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7111 (mp10) REVERT: p 92 LYS cc_start: 0.6627 (mttt) cc_final: 0.6319 (mmtt) REVERT: i 74 GLU cc_start: 0.8073 (pm20) cc_final: 0.7771 (pm20) REVERT: i 75 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8450 (mmmt) REVERT: i 92 LYS cc_start: 0.8738 (mtpt) cc_final: 0.8404 (mtpt) REVERT: i 119 LEU cc_start: 0.9241 (tp) cc_final: 0.8987 (mt) REVERT: k 10 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7620 (ttt90) REVERT: k 24 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8114 (tm-30) REVERT: k 115 LYS cc_start: 0.8873 (mmtt) cc_final: 0.8559 (mmtp) REVERT: k 130 MET cc_start: 0.8946 (tpp) cc_final: 0.8583 (tpp) REVERT: n 106 ARG cc_start: 0.8596 (mtm-85) cc_final: 0.8198 (mtm180) REVERT: n 117 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8555 (mm-40) REVERT: n 121 THR cc_start: 0.9137 (m) cc_final: 0.8866 (m) REVERT: n 128 LYS cc_start: 0.8030 (mmtt) cc_final: 0.7815 (mmtt) outliers start: 54 outliers final: 42 residues processed: 498 average time/residue: 0.2416 time to fit residues: 165.9073 Evaluate side-chains 506 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 461 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain 5 residue 324 ASN Chi-restraints excluded: chain 6 residue 316 LEU Chi-restraints excluded: chain f residue 48 VAL 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 107 SER Chi-restraints excluded: chain f residue 124 SER Chi-restraints excluded: chain h residue 14 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 84 ASP 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 18 SER Chi-restraints excluded: chain p residue 22 ASN 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 38 ASP Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain i residue 93 MET 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 117 GLN Chi-restraints excluded: chain n residue 120 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 96 optimal weight: 0.1980 chunk 63 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 101 optimal weight: 3.9990 chunk 111 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 113 GLN g 115 ASN j 30 ASN l 108 GLN m 32 ASN o 23 GLN k 132 ASN n 117 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.130764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.111082 restraints weight = 18821.419| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.73 r_work: 0.3389 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4239 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= 0.124 Angle : 0.584 9.992 14982 Z= 0.282 Chirality : 0.038 0.162 1783 Planarity : 0.003 0.032 2002 Dihedral : 4.118 58.651 1564 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.68 % Allowed : 23.12 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.24), residues: 1358 helix: 3.42 (0.19), residues: 730 sheet: -1.50 (0.41), residues: 137 loop : 1.02 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.001 PHE o 109 TYR 0.018 0.001 TYR l 116 ARG 0.005 0.000 ARG o 22 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 653) hydrogen bonds : angle 3.26646 ( 1926) covalent geometry : bond 0.00276 (11043) covalent geometry : angle 0.58431 (14982) *********************** 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 530 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 477 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 325 GLU cc_start: 0.7787 (pm20) cc_final: 0.7463 (pm20) REVERT: f 102 MET cc_start: 0.8834 (mmm) cc_final: 0.8585 (mmm) REVERT: g 22 ASN cc_start: 0.8960 (m-40) cc_final: 0.8539 (m110) REVERT: g 123 LYS cc_start: 0.8752 (tttp) cc_final: 0.8385 (ttpp) REVERT: g 126 MET cc_start: 0.8579 (mmm) cc_final: 0.8129 (mtt) REVERT: g 128 LYS cc_start: 0.8930 (ttpt) cc_final: 0.8437 (ttpt) REVERT: h 93 MET cc_start: 0.8743 (mmm) cc_final: 0.8434 (mmt) REVERT: h 116 ILE cc_start: 0.9346 (mm) cc_final: 0.9134 (mt) REVERT: j 126 MET cc_start: 0.9314 (mmm) cc_final: 0.9042 (mtt) REVERT: l 12 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8204 (mm110) REVERT: l 14 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8378 (mp0) REVERT: l 17 ASN cc_start: 0.8653 (t0) cc_final: 0.8350 (t0) REVERT: l 87 TYR cc_start: 0.8331 (m-80) cc_final: 0.8111 (m-80) REVERT: l 131 MET cc_start: 0.8933 (tpp) cc_final: 0.8519 (tpp) REVERT: m 4 ARG cc_start: 0.5229 (OUTLIER) cc_final: 0.4788 (mtt180) REVERT: m 14 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: m 23 GLN cc_start: 0.8912 (tp-100) cc_final: 0.8074 (tp40) REVERT: m 87 TYR cc_start: 0.8846 (m-80) cc_final: 0.8557 (m-10) REVERT: m 96 ASP cc_start: 0.8702 (p0) cc_final: 0.8472 (p0) REVERT: m 130 MET cc_start: 0.9127 (tpp) cc_final: 0.8712 (tpp) REVERT: m 135 GLN cc_start: 0.7967 (mp10) cc_final: 0.7464 (mp10) REVERT: o 102 MET cc_start: 0.7507 (mmp) cc_final: 0.7172 (tmm) REVERT: o 107 THR cc_start: 0.9228 (m) cc_final: 0.8873 (p) REVERT: o 108 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8674 (mm-40) REVERT: o 115 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8507 (mtmt) REVERT: o 132 ASN cc_start: 0.8735 (t0) cc_final: 0.8435 (t0) REVERT: o 135 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7104 (mp10) REVERT: p 92 LYS cc_start: 0.6647 (mttt) cc_final: 0.6321 (mmtt) REVERT: p 93 MET cc_start: 0.8438 (mmm) cc_final: 0.8101 (mmt) REVERT: p 123 LYS cc_start: 0.8273 (tptm) cc_final: 0.7705 (tptm) REVERT: i 75 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8414 (mmmt) REVERT: i 92 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8532 (mtpt) REVERT: i 119 LEU cc_start: 0.9224 (tp) cc_final: 0.8979 (mt) REVERT: k 10 ARG cc_start: 0.7879 (ttp80) cc_final: 0.7364 (tpt-90) REVERT: k 51 LYS cc_start: 0.8446 (tptp) cc_final: 0.8158 (tppt) REVERT: k 115 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8574 (mmtp) REVERT: k 130 MET cc_start: 0.8954 (tpp) cc_final: 0.8585 (tpp) REVERT: n 106 ARG cc_start: 0.8548 (mtm-85) cc_final: 0.8113 (mtm180) REVERT: n 117 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8632 (mm-40) REVERT: n 121 THR cc_start: 0.9099 (m) cc_final: 0.8823 (m) REVERT: n 128 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7814 (mmtt) outliers start: 53 outliers final: 44 residues processed: 502 average time/residue: 0.2340 time to fit residues: 162.4610 Evaluate side-chains 507 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 460 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 316 LEU Chi-restraints excluded: chain 7 residue 319 GLN Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain f residue 107 SER Chi-restraints excluded: chain f residue 124 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 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 84 ASP 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 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 38 ASP Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain i residue 93 MET 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 12 GLN Chi-restraints excluded: chain n residue 117 GLN Chi-restraints excluded: chain n residue 120 LEU 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 52 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 131 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- 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 m 32 ASN o 23 GLN p 22 ASN k 132 ASN n 112 ASN ** n 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.130608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.110869 restraints weight = 18444.580| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.70 r_work: 0.3387 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4365 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= 0.127 Angle : 0.604 14.364 14982 Z= 0.291 Chirality : 0.038 0.172 1783 Planarity : 0.003 0.033 2002 Dihedral : 4.087 59.773 1563 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.21 % Allowed : 22.95 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.23), residues: 1358 helix: 3.42 (0.18), residues: 730 sheet: -1.53 (0.42), residues: 132 loop : 1.05 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE l 45 TYR 0.017 0.001 TYR n 116 ARG 0.004 0.000 ARG o 22 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 653) hydrogen bonds : angle 3.27120 ( 1926) covalent geometry : bond 0.00287 (11043) covalent geometry : angle 0.60409 (14982) *********************** 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 531 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 472 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 325 GLU cc_start: 0.7761 (pm20) cc_final: 0.7397 (pm20) REVERT: g 22 ASN cc_start: 0.8949 (m-40) cc_final: 0.8532 (m110) REVERT: g 123 LYS cc_start: 0.8735 (tttp) cc_final: 0.8360 (ttpp) REVERT: g 126 MET cc_start: 0.8688 (mmm) cc_final: 0.8371 (mtt) REVERT: g 128 LYS cc_start: 0.8932 (ttpt) cc_final: 0.8439 (ttpt) REVERT: h 93 MET cc_start: 0.8710 (mmm) cc_final: 0.8403 (mmt) REVERT: h 116 ILE cc_start: 0.9350 (mm) cc_final: 0.9139 (mt) REVERT: j 113 GLN cc_start: 0.8402 (mt0) cc_final: 0.7943 (mt0) REVERT: j 126 MET cc_start: 0.9312 (mmm) cc_final: 0.9042 (mtt) REVERT: l 12 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8178 (mm110) REVERT: l 14 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8358 (mp0) REVERT: l 17 ASN cc_start: 0.8649 (t0) cc_final: 0.8351 (t0) REVERT: l 87 TYR cc_start: 0.8317 (m-80) cc_final: 0.8092 (m-80) REVERT: l 131 MET cc_start: 0.8927 (tpp) cc_final: 0.8511 (tpp) REVERT: m 4 ARG cc_start: 0.4785 (OUTLIER) cc_final: 0.4356 (mtt180) REVERT: m 14 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: m 23 GLN cc_start: 0.8973 (tp-100) cc_final: 0.8141 (tp40) REVERT: m 96 ASP cc_start: 0.8707 (p0) cc_final: 0.8480 (p0) REVERT: m 130 MET cc_start: 0.9104 (tpp) cc_final: 0.8689 (tpp) REVERT: m 132 ASN cc_start: 0.9289 (p0) cc_final: 0.8960 (p0) REVERT: m 135 GLN cc_start: 0.8066 (mp10) cc_final: 0.7559 (mp10) REVERT: o 102 MET cc_start: 0.7545 (mmp) cc_final: 0.7188 (tmm) REVERT: o 107 THR cc_start: 0.9229 (m) cc_final: 0.8880 (p) REVERT: o 108 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8690 (mm-40) REVERT: o 115 LYS cc_start: 0.8967 (mmmm) cc_final: 0.8372 (mtmt) REVERT: o 135 GLN cc_start: 0.7759 (mm-40) cc_final: 0.7525 (mp10) REVERT: p 92 LYS cc_start: 0.6681 (mttt) cc_final: 0.6216 (mmtt) REVERT: p 93 MET cc_start: 0.8455 (mmm) cc_final: 0.8097 (mmt) REVERT: p 123 LYS cc_start: 0.8273 (tptm) cc_final: 0.7679 (tptm) REVERT: i 75 LYS cc_start: 0.8668 (mmtt) cc_final: 0.8328 (mmmt) REVERT: i 92 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8327 (mtpt) REVERT: i 119 LEU cc_start: 0.9220 (tp) cc_final: 0.8975 (mt) REVERT: k 10 ARG cc_start: 0.7852 (ttp80) cc_final: 0.7318 (tpt-90) REVERT: k 51 LYS cc_start: 0.8432 (tptp) cc_final: 0.8099 (tppt) REVERT: k 115 LYS cc_start: 0.8900 (mmtt) cc_final: 0.8582 (mmtp) REVERT: k 130 MET cc_start: 0.8924 (tpp) cc_final: 0.8549 (tpp) REVERT: n 14 GLU cc_start: 0.7813 (pm20) cc_final: 0.7520 (pm20) REVERT: n 106 ARG cc_start: 0.8494 (mtm-85) cc_final: 0.8083 (mtm180) REVERT: n 121 THR cc_start: 0.9125 (m) cc_final: 0.8873 (m) outliers start: 59 outliers final: 50 residues processed: 501 average time/residue: 0.2337 time to fit residues: 161.6232 Evaluate side-chains 512 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 460 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain 6 residue 316 LEU Chi-restraints excluded: chain 7 residue 319 GLN 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 107 SER Chi-restraints excluded: chain f residue 132 LEU 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 23 VAL 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 126 MET Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain l residue 24 GLU Chi-restraints excluded: chain l residue 54 VAL Chi-restraints excluded: chain l residue 83 VAL Chi-restraints excluded: chain l residue 84 ASP 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 103 ASP 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 18 SER 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 23 VAL Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain i residue 93 MET 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 12 GLN Chi-restraints excluded: chain n residue 120 LEU Chi-restraints excluded: chain n residue 133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 113 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 0.0470 chunk 9 optimal weight: 0.9980 overall best weight: 0.8082 ------------------------------------------------------------------------------- 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 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.129325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.110188 restraints weight = 18533.350| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.63 r_work: 0.3398 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11043 Z= 0.128 Angle : 0.613 14.011 14982 Z= 0.294 Chirality : 0.038 0.161 1783 Planarity : 0.003 0.031 2002 Dihedral : 4.113 59.718 1563 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.03 % Allowed : 22.42 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.23), residues: 1358 helix: 3.38 (0.19), residues: 732 sheet: -1.53 (0.44), residues: 109 loop : 1.07 (0.29), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.001 PHE o 109 TYR 0.020 0.001 TYR k 116 ARG 0.006 0.000 ARG o 22 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 653) hydrogen bonds : angle 3.28195 ( 1926) covalent geometry : bond 0.00288 (11043) covalent geometry : angle 0.61287 (14982) *********************** 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 526 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 469 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 325 GLU cc_start: 0.7754 (pm20) cc_final: 0.7399 (pm20) REVERT: g 22 ASN cc_start: 0.8940 (m-40) cc_final: 0.8535 (m110) REVERT: g 38 ASP cc_start: 0.7855 (t0) cc_final: 0.7203 (p0) REVERT: g 123 LYS cc_start: 0.8756 (tttp) cc_final: 0.8374 (ttpp) REVERT: g 126 MET cc_start: 0.8640 (mmm) cc_final: 0.8358 (mtt) REVERT: g 128 LYS cc_start: 0.8939 (ttpt) cc_final: 0.8437 (ttpt) REVERT: h 93 MET cc_start: 0.8671 (mmm) cc_final: 0.8354 (mmt) REVERT: h 116 ILE cc_start: 0.9361 (mm) cc_final: 0.9161 (mt) REVERT: j 82 ASN cc_start: 0.8797 (t0) cc_final: 0.8155 (t0) REVERT: j 113 GLN cc_start: 0.8373 (mt0) cc_final: 0.7927 (mt0) REVERT: j 126 MET cc_start: 0.9288 (mmm) cc_final: 0.9032 (mtt) REVERT: l 12 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8188 (mm110) REVERT: l 14 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8361 (mp0) REVERT: l 17 ASN cc_start: 0.8658 (t0) cc_final: 0.8347 (t0) REVERT: l 112 ASN cc_start: 0.8715 (m110) cc_final: 0.8498 (m-40) REVERT: l 131 MET cc_start: 0.8911 (tpp) cc_final: 0.8508 (tpp) REVERT: m 4 ARG cc_start: 0.4799 (OUTLIER) cc_final: 0.4086 (mtt180) REVERT: m 14 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: m 23 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8121 (tp40) REVERT: m 41 ARG cc_start: 0.8966 (mmm-85) cc_final: 0.8465 (mmt-90) REVERT: m 96 ASP cc_start: 0.8691 (p0) cc_final: 0.8476 (p0) REVERT: m 130 MET cc_start: 0.9063 (tpp) cc_final: 0.8655 (tpp) REVERT: m 135 GLN cc_start: 0.8022 (mp10) cc_final: 0.7554 (mp10) REVERT: o 107 THR cc_start: 0.9221 (m) cc_final: 0.8863 (p) REVERT: o 108 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8754 (mm-40) REVERT: o 115 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8537 (mtmt) REVERT: o 135 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7167 (mp10) REVERT: p 92 LYS cc_start: 0.6614 (mttt) cc_final: 0.5240 (mmtm) REVERT: p 93 MET cc_start: 0.8459 (mmm) cc_final: 0.8103 (mmt) REVERT: p 123 LYS cc_start: 0.8270 (tptm) cc_final: 0.7700 (tptm) REVERT: i 3 LEU cc_start: 0.7817 (tt) cc_final: 0.7580 (tt) REVERT: i 74 GLU cc_start: 0.8171 (pm20) cc_final: 0.7758 (pm20) REVERT: i 75 LYS cc_start: 0.8690 (mmtt) cc_final: 0.8359 (mmmt) REVERT: i 92 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8395 (mtpt) REVERT: i 119 LEU cc_start: 0.9240 (tp) cc_final: 0.9003 (mt) REVERT: k 10 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7391 (tpt-90) REVERT: k 115 LYS cc_start: 0.8873 (mmtt) cc_final: 0.8566 (mmtp) REVERT: k 130 MET cc_start: 0.8863 (tpp) cc_final: 0.8480 (tpp) REVERT: n 106 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.8084 (mtm180) REVERT: n 117 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8633 (mm-40) REVERT: n 121 THR cc_start: 0.9088 (m) cc_final: 0.8826 (m) outliers start: 57 outliers final: 50 residues processed: 497 average time/residue: 0.2310 time to fit residues: 158.6198 Evaluate side-chains 516 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 464 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 107 SER Chi-restraints excluded: chain f residue 124 SER Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain g residue 51 VAL 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 23 VAL 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 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 24 GLU Chi-restraints excluded: chain l residue 54 VAL Chi-restraints excluded: chain l residue 83 VAL 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 118 MET Chi-restraints excluded: chain o residue 121 THR Chi-restraints excluded: chain p residue 14 LEU Chi-restraints excluded: chain p residue 18 SER 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 23 VAL Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain i residue 91 VAL 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 12 GLN Chi-restraints excluded: chain n residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 59 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 l 108 GLN k 132 ASN n 23 GLN ** n 112 ASN ** 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 = 0.3762 r_free = 0.3762 target = 0.127910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.109004 restraints weight = 18351.257| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.58 r_work: 0.3380 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11043 Z= 0.142 Angle : 0.639 13.717 14982 Z= 0.305 Chirality : 0.039 0.165 1783 Planarity : 0.003 0.036 2002 Dihedral : 4.172 59.209 1563 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.59 % Allowed : 23.74 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.24), residues: 1358 helix: 3.34 (0.19), residues: 733 sheet: -1.57 (0.43), residues: 123 loop : 1.12 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE l 45 TYR 0.016 0.001 TYR m 87 ARG 0.009 0.001 ARG j 43 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 653) hydrogen bonds : angle 3.33997 ( 1926) covalent geometry : bond 0.00324 (11043) covalent geometry : angle 0.63854 (14982) ********************** 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 512 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 460 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 325 GLU cc_start: 0.7805 (pm20) cc_final: 0.7453 (pm20) REVERT: f 45 LYS cc_start: 0.8804 (pttt) cc_final: 0.8195 (pttm) REVERT: f 46 GLN cc_start: 0.8833 (mp10) cc_final: 0.8593 (pm20) REVERT: g 22 ASN cc_start: 0.8963 (m-40) cc_final: 0.8553 (m110) REVERT: g 38 ASP cc_start: 0.7813 (t0) cc_final: 0.7329 (p0) REVERT: g 123 LYS cc_start: 0.8743 (tttp) cc_final: 0.8352 (ttpp) REVERT: g 126 MET cc_start: 0.8572 (mmm) cc_final: 0.8285 (mtt) REVERT: g 128 LYS cc_start: 0.8955 (ttpt) cc_final: 0.8455 (ttpt) REVERT: h 78 TYR cc_start: 0.9064 (t80) cc_final: 0.8629 (t80) REVERT: h 93 MET cc_start: 0.8697 (mmm) cc_final: 0.8370 (mmt) REVERT: h 116 ILE cc_start: 0.9364 (mm) cc_final: 0.9158 (mt) REVERT: j 82 ASN cc_start: 0.8718 (t0) cc_final: 0.8015 (t0) REVERT: j 88 ASN cc_start: 0.8668 (m110) cc_final: 0.8374 (m-40) REVERT: j 113 GLN cc_start: 0.8539 (mt0) cc_final: 0.8135 (mt0) REVERT: j 126 MET cc_start: 0.9282 (mmm) cc_final: 0.9042 (mtt) REVERT: j 128 LYS cc_start: 0.8788 (mtpt) cc_final: 0.8512 (ttpt) REVERT: l 12 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8173 (mm110) REVERT: l 14 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8392 (mp0) REVERT: l 17 ASN cc_start: 0.8698 (t0) cc_final: 0.8352 (t0) REVERT: l 22 ARG cc_start: 0.8810 (ttt90) cc_final: 0.8589 (ttt90) REVERT: l 131 MET cc_start: 0.8911 (tpp) cc_final: 0.8518 (tpp) REVERT: m 4 ARG cc_start: 0.4814 (OUTLIER) cc_final: 0.4093 (mtt-85) REVERT: m 14 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: m 23 GLN cc_start: 0.8969 (tp-100) cc_final: 0.8114 (tp40) REVERT: m 41 ARG cc_start: 0.8901 (mmm-85) cc_final: 0.8542 (mmt-90) REVERT: m 130 MET cc_start: 0.9089 (tpp) cc_final: 0.8698 (tpp) REVERT: m 135 GLN cc_start: 0.8082 (mp10) cc_final: 0.7384 (mp10) REVERT: o 107 THR cc_start: 0.9236 (m) cc_final: 0.8887 (p) REVERT: o 108 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8741 (mm-40) REVERT: o 115 LYS cc_start: 0.8961 (mmmm) cc_final: 0.8548 (mtmt) REVERT: o 135 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7219 (mp10) REVERT: p 92 LYS cc_start: 0.6627 (mttt) cc_final: 0.5278 (mmtm) REVERT: p 93 MET cc_start: 0.8523 (mmm) cc_final: 0.8150 (mmt) REVERT: p 123 LYS cc_start: 0.8266 (tptm) cc_final: 0.7650 (tptm) REVERT: i 74 GLU cc_start: 0.8251 (pm20) cc_final: 0.7882 (pm20) REVERT: i 75 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8389 (mmmt) REVERT: i 92 LYS cc_start: 0.8715 (mtpt) cc_final: 0.8406 (mtpt) REVERT: i 119 LEU cc_start: 0.9232 (tp) cc_final: 0.8979 (mt) REVERT: k 10 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7315 (tpt-90) REVERT: k 51 LYS cc_start: 0.8588 (tptp) cc_final: 0.8370 (tppt) REVERT: k 115 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8581 (mmtp) REVERT: k 130 MET cc_start: 0.8888 (tpp) cc_final: 0.8513 (tpp) REVERT: n 106 ARG cc_start: 0.8456 (mtm-85) cc_final: 0.8083 (mtm180) REVERT: n 117 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8457 (mm-40) REVERT: n 121 THR cc_start: 0.9127 (m) cc_final: 0.8885 (m) outliers start: 52 outliers final: 45 residues processed: 491 average time/residue: 0.2298 time to fit residues: 155.8756 Evaluate side-chains 502 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 455 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 107 SER Chi-restraints excluded: chain f residue 124 SER Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain g residue 51 VAL Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain h residue 14 LEU Chi-restraints excluded: chain h residue 23 VAL 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 126 MET Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain l residue 54 VAL Chi-restraints excluded: chain l residue 83 VAL 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 p residue 18 SER 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 23 VAL Chi-restraints excluded: chain i residue 38 ASP Chi-restraints excluded: chain i residue 91 VAL 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 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 120 LEU Chi-restraints excluded: chain n residue 133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 101 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 chunk 11 optimal weight: 0.0370 chunk 136 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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 o 23 GLN p 22 ASN p 40 GLN k 132 ASN ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 112 ASN ** 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 = 0.3791 r_free = 0.3791 target = 0.130868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.111182 restraints weight = 18350.181| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.68 r_work: 0.3386 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4676 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= 0.128 Angle : 0.642 13.865 14982 Z= 0.305 Chirality : 0.039 0.165 1783 Planarity : 0.003 0.040 2002 Dihedral : 4.154 59.262 1563 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.97 % Allowed : 24.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.24), residues: 1358 helix: 3.40 (0.19), residues: 732 sheet: -1.50 (0.42), residues: 128 loop : 1.13 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.002 PHE o 11 TYR 0.020 0.001 TYR k 116 ARG 0.009 0.000 ARG j 43 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 653) hydrogen bonds : angle 3.27193 ( 1926) covalent geometry : bond 0.00288 (11043) covalent geometry : angle 0.64220 (14982) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5819.66 seconds wall clock time: 100 minutes 46.42 seconds (6046.42 seconds total)