Starting phenix.real_space_refine on Thu Feb 15 02:28:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg0_30348/02_2024/7cg0_30348.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg0_30348/02_2024/7cg0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg0_30348/02_2024/7cg0_30348.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg0_30348/02_2024/7cg0_30348.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg0_30348/02_2024/7cg0_30348.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg0_30348/02_2024/7cg0_30348.pdb" } 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 Residue "g PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 117": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.74, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 4.37 Conformation dependent library (CDL) restraints added in 1.9 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: 0.90 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: 2.54 Time building geometry restraints manager: 4.78 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: 99.78 - 105.56: 326 105.56 - 111.35: 4757 111.35 - 117.13: 2936 117.13 - 122.92: 6294 122.92 - 128.70: 669 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 2.520 nonbonded pdb=" OG1 THR 9 330 " pdb=" OD1 ASP j 38 " model vdw 2.155 2.440 nonbonded pdb=" OG SER h 12 " pdb=" O VAL h 62 " model vdw 2.172 2.440 nonbonded pdb=" OH TYR o 116 " pdb=" OG1 THR p 129 " model vdw 2.289 2.440 nonbonded pdb=" OD1 ASN h 27 " pdb=" OH TYR h 42 " model vdw 2.292 2.440 ... (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 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: 7.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 27.450 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 29.410 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.910 ------------------------------------------------------------------------------- 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= 0.221 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 *********************** 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 fitting. rotamer outliers: 29 poor density : 561 time to evaluate : 1.211 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: 0.2387 time to fit residues: 187.2238 Evaluate side-chains 453 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 444 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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: 0.5980 chunk 104 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 324 ASN f 30 ASN f 88 ASN g 27 ASN g 104 ASN g 113 GLN h 22 ASN j 30 ASN j 115 ASN l 21 GLN ** l 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN ** o 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 30 ASN k 32 ASN k 92 GLN k 132 ASN n 112 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11043 Z= 0.279 Angle : 0.586 6.968 14982 Z= 0.295 Chirality : 0.041 0.168 1783 Planarity : 0.004 0.045 2002 Dihedral : 4.630 57.152 1574 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.83 % Allowed : 17.30 % Favored : 76.88 % 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: 3.23 (0.24), residues: 1358 helix: 3.70 (0.19), residues: 718 sheet: -1.84 (0.39), residues: 134 loop : 1.07 (0.30), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE o 11 TYR 0.019 0.002 TYR g 78 ARG 0.011 0.001 ARG f 43 *********************** 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 529 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 463 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: f 45 LYS cc_start: 0.8763 (ptpp) cc_final: 0.8460 (pttt) REVERT: f 123 LYS cc_start: 0.9064 (ttpt) cc_final: 0.8795 (tttt) REVERT: g 22 ASN cc_start: 0.8544 (m-40) cc_final: 0.8123 (m-40) REVERT: g 45 LYS cc_start: 0.8222 (ptpp) cc_final: 0.7593 (mttp) REVERT: g 123 LYS cc_start: 0.8543 (tttp) cc_final: 0.8144 (ttpp) REVERT: g 128 LYS cc_start: 0.8706 (ttpt) cc_final: 0.8393 (ttpt) REVERT: h 30 ASN cc_start: 0.9173 (m-40) cc_final: 0.8943 (m110) REVERT: h 97 ASP cc_start: 0.8486 (p0) cc_final: 0.8115 (p0) REVERT: h 102 MET cc_start: 0.8299 (mmm) cc_final: 0.8032 (mmt) REVERT: h 116 ILE cc_start: 0.9351 (mm) cc_final: 0.9062 (mt) REVERT: j 113 GLN cc_start: 0.7991 (mt0) cc_final: 0.7702 (mt0) REVERT: l 12 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7974 (mm-40) REVERT: l 17 ASN cc_start: 0.8536 (t0) cc_final: 0.8239 (t0) REVERT: l 26 LEU cc_start: 0.8864 (mt) cc_final: 0.8640 (mm) REVERT: l 86 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8509 (pp) REVERT: l 131 MET cc_start: 0.8816 (tpp) cc_final: 0.8348 (tpp) REVERT: m 4 ARG cc_start: 0.4726 (OUTLIER) cc_final: 0.4376 (mtt180) REVERT: m 5 LEU cc_start: 0.7322 (tp) cc_final: 0.7078 (tp) REVERT: m 14 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: m 23 GLN cc_start: 0.8913 (tp-100) cc_final: 0.8656 (tp40) REVERT: m 24 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7641 (tm-30) REVERT: m 25 ILE cc_start: 0.9307 (mt) cc_final: 0.9078 (mt) REVERT: m 41 ARG cc_start: 0.8859 (mmm-85) cc_final: 0.8593 (mmm-85) REVERT: m 96 ASP cc_start: 0.8347 (p0) cc_final: 0.8142 (p0) REVERT: m 128 LYS cc_start: 0.8791 (tppt) cc_final: 0.8572 (mmtt) REVERT: m 130 MET cc_start: 0.8993 (tpp) cc_final: 0.8636 (tpp) REVERT: o 104 ARG cc_start: 0.7887 (ttm-80) cc_final: 0.7388 (ttm-80) REVERT: o 107 THR cc_start: 0.9021 (m) cc_final: 0.8605 (p) REVERT: o 108 GLN cc_start: 0.8493 (mm-40) cc_final: 0.8174 (mm-40) REVERT: o 112 ASN cc_start: 0.8704 (t0) cc_final: 0.8462 (t0) REVERT: o 115 LYS cc_start: 0.8615 (mmmm) cc_final: 0.7855 (mtmt) REVERT: p 128 LYS cc_start: 0.9168 (mmtm) cc_final: 0.8923 (mmtm) REVERT: i 92 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8085 (mtpt) REVERT: i 102 MET cc_start: 0.8498 (mmm) cc_final: 0.8282 (mmm) REVERT: k 24 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7758 (tm-30) REVERT: k 118 MET cc_start: 0.8742 (tmm) cc_final: 0.8429 (tmm) REVERT: k 130 MET cc_start: 0.8440 (tpp) cc_final: 0.8086 (tpp) REVERT: n 18 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8085 (tt) REVERT: n 106 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7956 (mtm180) REVERT: n 112 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8558 (t0) outliers start: 66 outliers final: 41 residues processed: 498 average time/residue: 0.2199 time to fit residues: 152.2481 Evaluate side-chains 496 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 449 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain f residue 5 ASN Chi-restraints excluded: chain f residue 12 SER Chi-restraints excluded: chain f residue 26 SER Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 109 SER Chi-restraints excluded: chain f residue 124 SER Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 109 SER 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 42 ASP 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 99 THR 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 118 MET Chi-restraints excluded: chain o residue 122 VAL Chi-restraints excluded: chain p residue 98 VAL Chi-restraints excluded: chain p residue 109 SER 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 122 VAL Chi-restraints excluded: chain i residue 130 LEU Chi-restraints excluded: chain k residue 99 THR Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 111 ASP Chi-restraints excluded: chain n residue 18 LEU Chi-restraints excluded: chain n residue 92 GLN Chi-restraints excluded: chain n residue 112 ASN Chi-restraints excluded: chain n residue 117 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 135 optimal weight: 0.0040 chunk 111 optimal weight: 0.0770 chunk 124 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 overall best weight: 1.2156 ------------------------------------------------------------------------------- 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 j 115 ASN l 108 GLN ** l 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN o 126 GLN ** p 22 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3398 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= 0.213 Angle : 0.542 7.888 14982 Z= 0.264 Chirality : 0.038 0.159 1783 Planarity : 0.003 0.041 2002 Dihedral : 4.214 56.442 1567 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.77 % Allowed : 20.39 % Favored : 74.85 % 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: 3.27 (0.24), residues: 1358 helix: 3.74 (0.19), residues: 719 sheet: -1.79 (0.39), residues: 132 loop : 1.03 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE o 11 TYR 0.015 0.001 TYR j 112 ARG 0.004 0.000 ARG o 19 *********************** 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 522 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 468 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 93 MET cc_start: 0.8769 (mmt) cc_final: 0.8539 (mmm) REVERT: f 102 MET cc_start: 0.8432 (mmm) cc_final: 0.8190 (mmm) REVERT: f 123 LYS cc_start: 0.9101 (ttpt) cc_final: 0.8815 (tttt) REVERT: f 128 LYS cc_start: 0.8983 (ttmm) cc_final: 0.8747 (ttmm) REVERT: g 22 ASN cc_start: 0.8528 (m-40) cc_final: 0.8074 (m110) REVERT: g 45 LYS cc_start: 0.8091 (ptpp) cc_final: 0.7416 (mttp) REVERT: g 123 LYS cc_start: 0.8607 (tttp) cc_final: 0.8163 (ttpp) REVERT: g 128 LYS cc_start: 0.8583 (ttpt) cc_final: 0.7859 (ttpt) REVERT: h 30 ASN cc_start: 0.9209 (m-40) cc_final: 0.8999 (m110) REVERT: h 97 ASP cc_start: 0.8453 (p0) cc_final: 0.8135 (p0) REVERT: h 102 MET cc_start: 0.8374 (mmm) cc_final: 0.8106 (mmt) REVERT: h 116 ILE cc_start: 0.9340 (mm) cc_final: 0.9107 (mt) REVERT: l 12 GLN cc_start: 0.8312 (mm-40) cc_final: 0.8031 (mm-40) REVERT: l 17 ASN cc_start: 0.8512 (t0) cc_final: 0.8221 (t0) REVERT: l 131 MET cc_start: 0.8838 (tpp) cc_final: 0.8343 (tpp) REVERT: m 4 ARG cc_start: 0.4707 (OUTLIER) cc_final: 0.4368 (mtt180) REVERT: m 5 LEU cc_start: 0.7164 (tp) cc_final: 0.6922 (tp) REVERT: m 14 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6625 (mp0) REVERT: m 23 GLN cc_start: 0.8899 (tp-100) cc_final: 0.8076 (tp40) REVERT: m 24 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7630 (tm-30) REVERT: m 25 ILE cc_start: 0.9317 (mt) cc_final: 0.9039 (mt) REVERT: m 87 TYR cc_start: 0.8535 (m-80) cc_final: 0.8196 (m-10) REVERT: m 96 ASP cc_start: 0.8335 (p0) cc_final: 0.8104 (p0) REVERT: m 128 LYS cc_start: 0.8794 (tppt) cc_final: 0.8582 (mmtm) REVERT: m 130 MET cc_start: 0.8955 (tpp) cc_final: 0.8588 (tpp) REVERT: o 104 ARG cc_start: 0.7804 (ttm-80) cc_final: 0.7372 (ttm-80) REVERT: o 107 THR cc_start: 0.9032 (m) cc_final: 0.8644 (p) REVERT: o 108 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8188 (mm-40) REVERT: o 115 LYS cc_start: 0.8674 (mmmm) cc_final: 0.7885 (mtmt) REVERT: p 113 GLN cc_start: 0.8261 (mt0) cc_final: 0.7975 (mt0) REVERT: p 128 LYS cc_start: 0.9239 (mmtm) cc_final: 0.8927 (mmtm) REVERT: i 74 GLU cc_start: 0.7990 (pm20) cc_final: 0.7686 (pm20) REVERT: i 92 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7795 (mtpt) REVERT: i 102 MET cc_start: 0.8481 (mmm) cc_final: 0.8220 (mmm) REVERT: i 125 MET cc_start: 0.8005 (mtp) cc_final: 0.7369 (mtp) REVERT: k 24 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7747 (tm-30) REVERT: k 118 MET cc_start: 0.8759 (tmm) cc_final: 0.8469 (tmm) REVERT: k 130 MET cc_start: 0.8435 (tpp) cc_final: 0.8108 (tpp) REVERT: n 106 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7918 (mtm180) REVERT: n 112 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8435 (t0) REVERT: n 132 ASN cc_start: 0.8793 (t0) cc_final: 0.8499 (t0) outliers start: 54 outliers final: 35 residues processed: 492 average time/residue: 0.2090 time to fit residues: 142.8944 Evaluate side-chains 495 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 456 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain 5 residue 318 ASN Chi-restraints excluded: chain 6 residue 316 LEU Chi-restraints excluded: chain f residue 5 ASN Chi-restraints excluded: chain f residue 48 VAL Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 109 SER Chi-restraints excluded: chain f residue 124 SER Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain l residue 42 ASP Chi-restraints excluded: chain l residue 83 VAL Chi-restraints excluded: chain l residue 99 THR Chi-restraints excluded: chain l residue 114 LEU Chi-restraints excluded: chain l residue 121 THR 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 28 LEU Chi-restraints excluded: chain p residue 48 VAL Chi-restraints excluded: chain p residue 99 VAL Chi-restraints excluded: chain p residue 109 SER Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain i residue 92 LYS Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain i residue 116 ILE Chi-restraints excluded: chain k residue 99 THR 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 92 GLN Chi-restraints excluded: chain n residue 112 ASN 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 124 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 65 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 h 22 ASN j 30 ASN j 115 ASN l 108 GLN ** l 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN ** p 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 92 GLN n 112 ASN ** n 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11043 Z= 0.329 Angle : 0.603 8.166 14982 Z= 0.299 Chirality : 0.041 0.156 1783 Planarity : 0.004 0.041 2002 Dihedral : 4.330 58.598 1564 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 6.71 % Allowed : 20.30 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.90 (0.23), residues: 1358 helix: 3.37 (0.19), residues: 727 sheet: -1.63 (0.41), residues: 113 loop : 0.71 (0.29), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE n 109 TYR 0.012 0.002 TYR h 112 ARG 0.004 0.001 ARG i 20 *********************** 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 544 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 468 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 102 MET cc_start: 0.8536 (mmm) cc_final: 0.8223 (mmm) REVERT: f 123 LYS cc_start: 0.9100 (ttpt) cc_final: 0.8843 (tttt) REVERT: g 22 ASN cc_start: 0.8557 (m-40) cc_final: 0.8076 (m110) REVERT: g 45 LYS cc_start: 0.8108 (ptpp) cc_final: 0.7446 (mttp) REVERT: g 106 MET cc_start: 0.7929 (mtt) cc_final: 0.7704 (mtt) REVERT: g 123 LYS cc_start: 0.8589 (tttp) cc_final: 0.8168 (ttpp) REVERT: g 128 LYS cc_start: 0.8745 (ttpt) cc_final: 0.8232 (ttpt) REVERT: h 75 LYS cc_start: 0.7524 (pttt) cc_final: 0.7210 (pptt) REVERT: h 97 ASP cc_start: 0.8425 (p0) cc_final: 0.8201 (p0) REVERT: j 113 GLN cc_start: 0.8260 (mt0) cc_final: 0.7865 (mt0) REVERT: l 12 GLN cc_start: 0.8339 (mm-40) cc_final: 0.8066 (mm110) REVERT: l 17 ASN cc_start: 0.8655 (t0) cc_final: 0.8332 (t0) REVERT: l 131 MET cc_start: 0.8857 (tpp) cc_final: 0.8340 (tpp) REVERT: m 4 ARG cc_start: 0.5400 (OUTLIER) cc_final: 0.4862 (mtt180) REVERT: m 14 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: m 23 GLN cc_start: 0.8895 (tp-100) cc_final: 0.7991 (tp40) REVERT: m 51 LYS cc_start: 0.8821 (mtpt) cc_final: 0.8534 (mtmt) REVERT: m 87 TYR cc_start: 0.8628 (m-80) cc_final: 0.8328 (m-10) REVERT: m 96 ASP cc_start: 0.8464 (p0) cc_final: 0.8247 (p0) REVERT: m 115 LYS cc_start: 0.9058 (mttm) cc_final: 0.8754 (mttm) REVERT: m 130 MET cc_start: 0.8984 (tpp) cc_final: 0.8572 (tpp) REVERT: o 23 GLN cc_start: 0.7753 (tp40) cc_final: 0.7479 (tp40) REVERT: o 104 ARG cc_start: 0.7895 (ttm-80) cc_final: 0.7402 (ttm-80) REVERT: o 107 THR cc_start: 0.9053 (m) cc_final: 0.8628 (p) REVERT: o 108 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8289 (mm-40) REVERT: o 115 LYS cc_start: 0.8694 (mmmm) cc_final: 0.7907 (mtmt) REVERT: o 123 LEU cc_start: 0.7978 (tp) cc_final: 0.7747 (tp) REVERT: p 43 ARG cc_start: 0.6404 (mtt180) cc_final: 0.6072 (ttt180) REVERT: p 113 GLN cc_start: 0.8282 (mt0) cc_final: 0.8056 (mt0) REVERT: p 128 LYS cc_start: 0.9243 (mmtm) cc_final: 0.8869 (mmtm) REVERT: i 74 GLU cc_start: 0.7983 (pm20) cc_final: 0.7738 (pm20) REVERT: i 75 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8191 (mmmt) REVERT: i 92 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8076 (mtpt) REVERT: i 119 LEU cc_start: 0.8950 (tp) cc_final: 0.8714 (mt) REVERT: i 123 LYS cc_start: 0.8105 (tttm) cc_final: 0.7862 (ttpt) REVERT: i 125 MET cc_start: 0.8321 (mtp) cc_final: 0.7684 (mtp) REVERT: k 10 ARG cc_start: 0.7430 (ttp80) cc_final: 0.7190 (ttt90) REVERT: k 24 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7772 (tm-30) REVERT: k 115 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8428 (mmtp) REVERT: k 118 MET cc_start: 0.8759 (tmm) cc_final: 0.8441 (tmm) REVERT: k 130 MET cc_start: 0.8438 (tpp) cc_final: 0.8146 (tpp) REVERT: n 14 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6740 (pm20) REVERT: n 53 MET cc_start: 0.7635 (mmm) cc_final: 0.7431 (mmm) REVERT: n 106 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7890 (mtm180) REVERT: n 112 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8441 (t0) REVERT: n 121 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8666 (m) outliers start: 76 outliers final: 56 residues processed: 506 average time/residue: 0.2444 time to fit residues: 170.7094 Evaluate side-chains 514 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 452 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain 5 residue 318 ASN Chi-restraints excluded: chain 6 residue 316 LEU Chi-restraints excluded: chain 7 residue 319 GLN Chi-restraints excluded: chain f residue 5 ASN Chi-restraints excluded: chain f residue 26 SER 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 109 SER Chi-restraints excluded: chain f residue 124 SER Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 109 SER Chi-restraints excluded: chain g residue 129 THR 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 91 VAL Chi-restraints excluded: chain h residue 122 VAL Chi-restraints excluded: chain h residue 129 THR Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain l residue 24 GLU Chi-restraints excluded: chain l residue 42 ASP Chi-restraints excluded: chain l residue 83 VAL Chi-restraints excluded: chain l residue 99 THR 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 99 THR Chi-restraints excluded: chain m residue 125 SER Chi-restraints excluded: chain m residue 135 GLN 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 51 VAL Chi-restraints excluded: chain p residue 98 VAL Chi-restraints excluded: chain p residue 99 VAL Chi-restraints excluded: chain p residue 109 SER Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain i residue 32 ASP Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain i residue 92 LYS Chi-restraints excluded: chain i residue 93 MET Chi-restraints excluded: chain i residue 99 VAL Chi-restraints excluded: chain i residue 122 VAL Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 99 THR Chi-restraints excluded: chain k residue 100 VAL Chi-restraints excluded: chain k residue 111 ASP Chi-restraints excluded: chain k residue 113 SER Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain n residue 34 ASP Chi-restraints excluded: chain n residue 92 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 h 22 ASN j 30 ASN l 23 GLN l 108 GLN l 112 ASN m 32 ASN p 22 ASN k 92 GLN n 17 ASN n 21 GLN ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11043 Z= 0.274 Angle : 0.597 11.839 14982 Z= 0.291 Chirality : 0.040 0.157 1783 Planarity : 0.004 0.044 2002 Dihedral : 4.335 59.105 1564 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 6.80 % Allowed : 21.62 % Favored : 71.58 % 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: 2.88 (0.24), residues: 1358 helix: 3.37 (0.19), residues: 728 sheet: -1.66 (0.40), residues: 122 loop : 0.71 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE n 109 TYR 0.013 0.002 TYR l 87 ARG 0.004 0.000 ARG m 41 *********************** 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 535 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 458 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 75 LYS cc_start: 0.8196 (mmtp) cc_final: 0.7913 (mmtp) REVERT: f 102 MET cc_start: 0.8534 (mmm) cc_final: 0.8186 (mmm) REVERT: f 123 LYS cc_start: 0.9106 (ttpt) cc_final: 0.8808 (tttt) REVERT: g 22 ASN cc_start: 0.8537 (m-40) cc_final: 0.8041 (m110) REVERT: g 123 LYS cc_start: 0.8620 (tttp) cc_final: 0.8186 (ttpp) REVERT: g 128 LYS cc_start: 0.8769 (ttpt) cc_final: 0.8476 (ttmt) REVERT: h 75 LYS cc_start: 0.7554 (pttt) cc_final: 0.7230 (pptt) REVERT: j 113 GLN cc_start: 0.8360 (mt0) cc_final: 0.7987 (mt0) REVERT: j 126 MET cc_start: 0.8905 (mmm) cc_final: 0.8636 (mtt) REVERT: l 12 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8071 (mm110) REVERT: l 14 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8127 (mp0) REVERT: l 17 ASN cc_start: 0.8674 (t0) cc_final: 0.8360 (t0) REVERT: l 131 MET cc_start: 0.8854 (tpp) cc_final: 0.8354 (tpp) REVERT: m 4 ARG cc_start: 0.5440 (OUTLIER) cc_final: 0.4956 (mtt180) REVERT: m 14 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: m 23 GLN cc_start: 0.8904 (tp-100) cc_final: 0.8030 (tp40) REVERT: m 51 LYS cc_start: 0.8746 (mtpt) cc_final: 0.8434 (mtmt) REVERT: m 130 MET cc_start: 0.8975 (tpp) cc_final: 0.8542 (tpp) REVERT: o 23 GLN cc_start: 0.7827 (tp40) cc_final: 0.7567 (tp40) REVERT: o 104 ARG cc_start: 0.7888 (ttm-80) cc_final: 0.7424 (mtt-85) REVERT: o 107 THR cc_start: 0.9056 (m) cc_final: 0.8645 (p) REVERT: o 108 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8308 (mm-40) REVERT: o 115 LYS cc_start: 0.8693 (mmmm) cc_final: 0.7921 (mtmt) REVERT: o 123 LEU cc_start: 0.8012 (tp) cc_final: 0.7811 (tp) REVERT: o 128 LYS cc_start: 0.6975 (ptpt) cc_final: 0.6680 (pttm) REVERT: o 135 GLN cc_start: 0.6173 (mp10) cc_final: 0.5922 (mp10) REVERT: p 43 ARG cc_start: 0.6387 (mtt180) cc_final: 0.6073 (ttt180) REVERT: p 128 LYS cc_start: 0.9200 (mmtm) cc_final: 0.8788 (mmtm) REVERT: i 75 LYS cc_start: 0.8468 (mmtt) cc_final: 0.8211 (mmmt) REVERT: i 119 LEU cc_start: 0.9008 (tp) cc_final: 0.8762 (mt) REVERT: i 123 LYS cc_start: 0.8261 (tttm) cc_final: 0.7883 (ttpp) REVERT: k 10 ARG cc_start: 0.7528 (ttp80) cc_final: 0.7294 (ttt90) REVERT: k 24 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7740 (tm-30) REVERT: k 115 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8407 (mmtp) REVERT: k 118 MET cc_start: 0.8744 (tmm) cc_final: 0.8459 (tmm) REVERT: k 130 MET cc_start: 0.8528 (tpp) cc_final: 0.8198 (tpp) REVERT: n 11 PHE cc_start: 0.7179 (t80) cc_final: 0.6831 (t80) REVERT: n 14 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6928 (pm20) REVERT: n 41 ARG cc_start: 0.9169 (mmm-85) cc_final: 0.8725 (mmt90) REVERT: n 106 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7902 (mtm180) REVERT: n 121 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8671 (m) outliers start: 77 outliers final: 65 residues processed: 496 average time/residue: 0.2307 time to fit residues: 158.2959 Evaluate side-chains 517 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 448 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain 5 residue 318 ASN Chi-restraints excluded: chain 5 residue 324 ASN Chi-restraints excluded: chain 6 residue 316 LEU Chi-restraints excluded: chain 7 residue 319 GLN Chi-restraints excluded: chain f residue 5 ASN Chi-restraints excluded: chain f residue 26 SER Chi-restraints excluded: chain f residue 48 VAL Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 109 SER Chi-restraints excluded: chain f residue 124 SER Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 99 VAL Chi-restraints excluded: chain g residue 109 SER Chi-restraints excluded: chain g residue 129 THR 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 122 VAL Chi-restraints excluded: chain h residue 126 MET Chi-restraints excluded: chain h residue 129 THR Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain l residue 42 ASP 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 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 99 THR Chi-restraints excluded: chain m residue 125 SER Chi-restraints excluded: chain m residue 135 GLN 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 109 SER Chi-restraints excluded: chain p residue 119 LEU Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain i residue 32 ASP 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 25 ILE Chi-restraints excluded: chain k residue 99 THR 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 5 LEU Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain n residue 34 ASP Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain n residue 92 GLN Chi-restraints excluded: chain n residue 96 ASP Chi-restraints excluded: chain n residue 117 GLN Chi-restraints excluded: chain n residue 121 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 46 GLN g 113 GLN g 115 ASN j 30 ASN m 32 ASN m 92 GLN p 22 ASN p 120 ASN k 132 ASN n 17 ASN n 21 GLN ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 112 ASN n 117 GLN n 126 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4373 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= 0.184 Angle : 0.554 11.269 14982 Z= 0.267 Chirality : 0.038 0.155 1783 Planarity : 0.003 0.036 2002 Dihedral : 4.156 56.408 1564 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 6.27 % Allowed : 22.33 % Favored : 71.40 % 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: 3.17 (0.24), residues: 1358 helix: 3.58 (0.19), residues: 731 sheet: -1.66 (0.41), residues: 119 loop : 0.90 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE o 109 TYR 0.019 0.001 TYR l 116 ARG 0.005 0.000 ARG m 41 *********************** 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 545 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 474 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 102 MET cc_start: 0.8327 (mmm) cc_final: 0.8074 (mmm) REVERT: f 123 LYS cc_start: 0.9071 (ttpt) cc_final: 0.8778 (tttt) REVERT: g 22 ASN cc_start: 0.8516 (m-40) cc_final: 0.8028 (m110) REVERT: g 123 LYS cc_start: 0.8589 (tttp) cc_final: 0.8150 (ttpp) REVERT: g 128 LYS cc_start: 0.8664 (ttpt) cc_final: 0.8437 (ttpt) REVERT: h 75 LYS cc_start: 0.7476 (pttt) cc_final: 0.7241 (pptt) REVERT: j 112 TYR cc_start: 0.8998 (t80) cc_final: 0.8784 (t80) REVERT: j 113 GLN cc_start: 0.8170 (mt0) cc_final: 0.7791 (mt0) REVERT: l 12 GLN cc_start: 0.8347 (mm-40) cc_final: 0.8081 (mm110) REVERT: l 14 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8114 (mp0) REVERT: l 17 ASN cc_start: 0.8578 (t0) cc_final: 0.8250 (t0) REVERT: l 131 MET cc_start: 0.8841 (tpp) cc_final: 0.8343 (tpp) REVERT: m 4 ARG cc_start: 0.4938 (OUTLIER) cc_final: 0.4624 (mtt180) REVERT: m 14 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: m 23 GLN cc_start: 0.8851 (tp-100) cc_final: 0.7973 (tp40) REVERT: m 41 ARG cc_start: 0.8808 (mmm-85) cc_final: 0.8588 (mmm-85) REVERT: m 51 LYS cc_start: 0.8752 (mtpt) cc_final: 0.8426 (mtmt) REVERT: m 115 LYS cc_start: 0.9000 (mttm) cc_final: 0.8718 (mttm) REVERT: m 130 MET cc_start: 0.8968 (tpp) cc_final: 0.8517 (tpp) REVERT: o 23 GLN cc_start: 0.7779 (tp40) cc_final: 0.7568 (tp40) REVERT: o 102 MET cc_start: 0.8575 (tmm) cc_final: 0.7641 (mmp) REVERT: o 104 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7429 (mtt-85) REVERT: o 107 THR cc_start: 0.9057 (m) cc_final: 0.8672 (p) REVERT: o 108 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8333 (mm-40) REVERT: o 115 LYS cc_start: 0.8703 (mmmm) cc_final: 0.7872 (mtmt) REVERT: o 123 LEU cc_start: 0.7962 (tp) cc_final: 0.7738 (tp) REVERT: o 135 GLN cc_start: 0.6520 (mp10) cc_final: 0.6178 (mp10) REVERT: p 43 ARG cc_start: 0.6348 (mtt180) cc_final: 0.6084 (ttt180) REVERT: p 93 MET cc_start: 0.8367 (mmm) cc_final: 0.7970 (mmt) REVERT: p 128 LYS cc_start: 0.9255 (mmtm) cc_final: 0.8866 (mmtm) REVERT: i 75 LYS cc_start: 0.8401 (mmtt) cc_final: 0.8153 (mmmt) REVERT: i 92 LYS cc_start: 0.8579 (mtpt) cc_final: 0.8144 (mtpt) REVERT: i 102 MET cc_start: 0.8393 (mmm) cc_final: 0.8152 (mmm) REVERT: i 119 LEU cc_start: 0.9020 (tp) cc_final: 0.8756 (mt) REVERT: i 125 MET cc_start: 0.8282 (mtm) cc_final: 0.8049 (mtp) REVERT: k 10 ARG cc_start: 0.7465 (ttp80) cc_final: 0.7085 (tpt-90) REVERT: k 102 MET cc_start: 0.7974 (tpp) cc_final: 0.7717 (mmt) REVERT: k 115 LYS cc_start: 0.8820 (mmtt) cc_final: 0.8440 (mmtp) REVERT: k 118 MET cc_start: 0.8715 (tmm) cc_final: 0.8455 (tmm) REVERT: k 130 MET cc_start: 0.8522 (tpp) cc_final: 0.8216 (tpp) REVERT: n 11 PHE cc_start: 0.6733 (t80) cc_final: 0.6472 (t80) REVERT: n 14 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6851 (pm20) REVERT: n 41 ARG cc_start: 0.9124 (mmm-85) cc_final: 0.8680 (mmt90) REVERT: n 106 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7832 (mtm180) outliers start: 71 outliers final: 53 residues processed: 507 average time/residue: 0.1980 time to fit residues: 138.4740 Evaluate side-chains 512 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 456 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain 5 residue 318 ASN Chi-restraints excluded: chain 6 residue 316 LEU Chi-restraints excluded: chain f residue 5 ASN Chi-restraints excluded: chain f residue 26 SER Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain f residue 107 SER Chi-restraints excluded: chain f residue 109 SER Chi-restraints excluded: chain g residue 51 VAL Chi-restraints excluded: chain g residue 109 SER Chi-restraints excluded: chain h residue 3 LEU Chi-restraints excluded: chain h residue 23 VAL Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 91 VAL Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain l residue 42 ASP 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 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 99 THR Chi-restraints excluded: chain m residue 125 SER Chi-restraints excluded: chain m residue 135 GLN 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 22 ASN 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 109 SER Chi-restraints excluded: chain p residue 119 LEU Chi-restraints excluded: chain p residue 130 LEU Chi-restraints excluded: chain 8 residue 324 ASN Chi-restraints excluded: chain i residue 23 VAL 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 k residue 99 THR 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 5 LEU Chi-restraints excluded: chain n residue 12 GLN Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain n residue 34 ASP Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain n residue 92 GLN Chi-restraints excluded: chain n residue 112 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 113 GLN g 115 ASN h 22 ASN h 46 GLN l 108 GLN m 32 ASN ** o 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 22 ASN k 92 GLN k 132 ASN n 17 ASN n 21 GLN ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 112 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11043 Z= 0.319 Angle : 0.628 11.346 14982 Z= 0.305 Chirality : 0.041 0.168 1783 Planarity : 0.004 0.039 2002 Dihedral : 4.292 55.584 1564 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 6.97 % Allowed : 22.33 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.87 (0.24), residues: 1358 helix: 3.36 (0.19), residues: 731 sheet: -1.78 (0.40), residues: 122 loop : 0.75 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE g 7 TYR 0.016 0.002 TYR m 87 ARG 0.006 0.001 ARG p 20 *********************** 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 544 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 465 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 102 MET cc_start: 0.8464 (mmm) cc_final: 0.8125 (mmm) REVERT: f 123 LYS cc_start: 0.9100 (ttpt) cc_final: 0.8817 (tttt) REVERT: g 22 ASN cc_start: 0.8549 (m-40) cc_final: 0.8053 (m110) REVERT: g 123 LYS cc_start: 0.8589 (tttp) cc_final: 0.8172 (ttpp) REVERT: h 75 LYS cc_start: 0.7546 (pttt) cc_final: 0.7233 (pptt) REVERT: j 88 ASN cc_start: 0.8595 (m110) cc_final: 0.8301 (m-40) REVERT: l 12 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8098 (mm110) REVERT: l 17 ASN cc_start: 0.8715 (t0) cc_final: 0.8414 (t0) REVERT: l 87 TYR cc_start: 0.8132 (m-80) cc_final: 0.7848 (m-80) REVERT: l 131 MET cc_start: 0.8855 (tpp) cc_final: 0.8360 (tpp) REVERT: m 4 ARG cc_start: 0.5373 (OUTLIER) cc_final: 0.4777 (mtt180) REVERT: m 23 GLN cc_start: 0.8863 (tp-100) cc_final: 0.7964 (tp40) REVERT: m 130 MET cc_start: 0.8995 (tpp) cc_final: 0.8591 (tpp) REVERT: o 23 GLN cc_start: 0.7820 (tp40) cc_final: 0.7376 (tp40) REVERT: o 102 MET cc_start: 0.8624 (tmm) cc_final: 0.7645 (mmp) REVERT: o 104 ARG cc_start: 0.7929 (ttm-80) cc_final: 0.7448 (ttm-80) REVERT: o 107 THR cc_start: 0.9086 (m) cc_final: 0.8663 (p) REVERT: o 108 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8349 (mm-40) REVERT: o 115 LYS cc_start: 0.8739 (mmmm) cc_final: 0.7912 (mtmt) REVERT: o 123 LEU cc_start: 0.8018 (tp) cc_final: 0.7790 (tp) REVERT: o 135 GLN cc_start: 0.6721 (mp10) cc_final: 0.6345 (mp10) REVERT: p 128 LYS cc_start: 0.9279 (mmtm) cc_final: 0.8876 (mmtm) REVERT: i 74 GLU cc_start: 0.8022 (pm20) cc_final: 0.7793 (pm20) REVERT: i 75 LYS cc_start: 0.8482 (mmtt) cc_final: 0.8219 (mmmt) REVERT: i 92 LYS cc_start: 0.8578 (mtpt) cc_final: 0.8058 (mtpt) REVERT: i 119 LEU cc_start: 0.9028 (tp) cc_final: 0.8765 (mt) REVERT: i 123 LYS cc_start: 0.8187 (tttm) cc_final: 0.7870 (ttpp) REVERT: k 10 ARG cc_start: 0.7444 (ttp80) cc_final: 0.7043 (tpt-90) REVERT: k 115 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8489 (mmtp) REVERT: k 118 MET cc_start: 0.8732 (tmm) cc_final: 0.8439 (tmm) REVERT: k 130 MET cc_start: 0.8508 (tpp) cc_final: 0.8200 (tpp) REVERT: n 14 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6717 (pm20) REVERT: n 41 ARG cc_start: 0.9159 (mmm-85) cc_final: 0.8677 (mmt90) REVERT: n 53 MET cc_start: 0.7426 (mmm) cc_final: 0.7147 (tpt) REVERT: n 106 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7891 (mtm180) outliers start: 79 outliers final: 66 residues processed: 505 average time/residue: 0.2007 time to fit residues: 139.8550 Evaluate side-chains 531 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 463 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain 5 residue 318 ASN Chi-restraints excluded: chain 5 residue 324 ASN Chi-restraints excluded: chain 6 residue 316 LEU Chi-restraints excluded: chain f residue 5 ASN Chi-restraints excluded: chain f residue 12 SER Chi-restraints excluded: chain f residue 26 SER Chi-restraints excluded: chain f residue 76 LEU Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain f residue 107 SER Chi-restraints excluded: chain f residue 109 SER Chi-restraints excluded: chain f residue 124 SER Chi-restraints excluded: chain g residue 51 VAL Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 99 VAL Chi-restraints excluded: chain g residue 109 SER Chi-restraints excluded: chain g residue 129 THR 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 91 VAL Chi-restraints excluded: chain h residue 122 VAL Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain l residue 24 GLU Chi-restraints excluded: chain l residue 42 ASP Chi-restraints excluded: chain l residue 54 VAL 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 30 ILE Chi-restraints excluded: chain m residue 99 THR Chi-restraints excluded: chain m residue 125 SER Chi-restraints excluded: chain m residue 135 GLN 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 32 ASP 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 25 ILE Chi-restraints excluded: chain k residue 99 THR 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 5 LEU Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain n residue 92 GLN Chi-restraints excluded: chain n residue 96 ASP Chi-restraints excluded: chain n residue 112 ASN 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 53 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 113 GLN h 22 ASN h 46 GLN m 21 GLN m 32 ASN ** o 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 22 ASN k 92 GLN k 132 ASN n 17 ASN n 21 GLN ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11043 Z= 0.194 Angle : 0.596 9.831 14982 Z= 0.285 Chirality : 0.038 0.174 1783 Planarity : 0.003 0.046 2002 Dihedral : 4.159 56.433 1564 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 6.09 % Allowed : 23.12 % Favored : 70.79 % 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: 3.09 (0.24), residues: 1358 helix: 3.52 (0.19), residues: 732 sheet: -1.76 (0.39), residues: 125 loop : 0.90 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.001 PHE n 109 TYR 0.019 0.001 TYR l 116 ARG 0.005 0.000 ARG o 22 *********************** 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 541 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 472 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: f 102 MET cc_start: 0.8371 (mmm) cc_final: 0.8130 (mmm) REVERT: f 123 LYS cc_start: 0.9084 (ttpt) cc_final: 0.8772 (tttt) REVERT: g 22 ASN cc_start: 0.8536 (m-40) cc_final: 0.8061 (m110) REVERT: g 123 LYS cc_start: 0.8574 (tttp) cc_final: 0.8130 (ttpp) REVERT: g 128 LYS cc_start: 0.8585 (ttmt) cc_final: 0.8094 (ttpt) REVERT: h 75 LYS cc_start: 0.7499 (pttt) cc_final: 0.7248 (pptt) REVERT: h 93 MET cc_start: 0.8653 (mmm) cc_final: 0.8315 (mmt) REVERT: j 82 ASN cc_start: 0.8755 (t0) cc_final: 0.8174 (t0) REVERT: j 88 ASN cc_start: 0.8531 (m110) cc_final: 0.8215 (m-40) REVERT: j 113 GLN cc_start: 0.8354 (mt0) cc_final: 0.7936 (mt0) REVERT: j 126 MET cc_start: 0.8831 (mmm) cc_final: 0.8591 (mtt) REVERT: l 12 GLN cc_start: 0.8359 (mm-40) cc_final: 0.8090 (mm110) REVERT: l 17 ASN cc_start: 0.8627 (t0) cc_final: 0.8273 (t0) REVERT: l 131 MET cc_start: 0.8837 (tpp) cc_final: 0.8347 (tpp) REVERT: m 4 ARG cc_start: 0.5279 (OUTLIER) cc_final: 0.4571 (mtt180) REVERT: m 14 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7454 (mp0) REVERT: m 21 GLN cc_start: 0.8709 (mt0) cc_final: 0.8407 (mt0) REVERT: m 23 GLN cc_start: 0.8811 (tp-100) cc_final: 0.7924 (tp40) REVERT: m 51 LYS cc_start: 0.8754 (mtpt) cc_final: 0.8507 (mtmt) REVERT: m 130 MET cc_start: 0.8963 (tpp) cc_final: 0.8548 (tpp) REVERT: o 23 GLN cc_start: 0.7741 (tp40) cc_final: 0.7383 (tp40) REVERT: o 102 MET cc_start: 0.8591 (tmm) cc_final: 0.7681 (mmp) REVERT: o 104 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.7383 (ttm-80) REVERT: o 107 THR cc_start: 0.9078 (m) cc_final: 0.8686 (p) REVERT: o 108 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8343 (mm-40) REVERT: o 115 LYS cc_start: 0.8704 (mmmm) cc_final: 0.8072 (mtmt) REVERT: o 123 LEU cc_start: 0.7996 (tp) cc_final: 0.7774 (tp) REVERT: o 135 GLN cc_start: 0.6910 (mp10) cc_final: 0.6563 (mp10) REVERT: i 74 GLU cc_start: 0.8077 (pm20) cc_final: 0.7854 (pm20) REVERT: i 75 LYS cc_start: 0.8421 (mmtt) cc_final: 0.8170 (mmmt) REVERT: i 92 LYS cc_start: 0.8605 (mtpt) cc_final: 0.8113 (mtpt) REVERT: i 119 LEU cc_start: 0.9030 (tp) cc_final: 0.8774 (mt) REVERT: i 125 MET cc_start: 0.8353 (mtm) cc_final: 0.8093 (mtp) REVERT: k 10 ARG cc_start: 0.7456 (ttp80) cc_final: 0.7079 (tpt-90) REVERT: k 102 MET cc_start: 0.8027 (tpp) cc_final: 0.7755 (mmt) REVERT: k 115 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8476 (mmtp) REVERT: k 118 MET cc_start: 0.8701 (tmm) cc_final: 0.8435 (tmm) REVERT: k 130 MET cc_start: 0.8492 (tpp) cc_final: 0.8056 (tpp) REVERT: n 14 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6634 (pm20) REVERT: n 121 THR cc_start: 0.8945 (m) cc_final: 0.8643 (m) outliers start: 69 outliers final: 56 residues processed: 505 average time/residue: 0.1805 time to fit residues: 126.2371 Evaluate side-chains 522 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 464 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 312 VAL Chi-restraints excluded: chain 5 residue 318 ASN Chi-restraints excluded: chain 6 residue 316 LEU Chi-restraints excluded: chain f residue 4 LEU Chi-restraints excluded: chain f residue 5 ASN Chi-restraints excluded: chain f residue 26 SER Chi-restraints excluded: chain f residue 76 LEU Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain f residue 107 SER Chi-restraints excluded: chain f residue 109 SER Chi-restraints excluded: chain g residue 51 VAL Chi-restraints excluded: chain g residue 109 SER Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain h residue 3 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 122 VAL Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain l residue 42 ASP 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 121 THR Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain m residue 30 ILE Chi-restraints excluded: chain m residue 99 THR Chi-restraints excluded: chain m residue 135 GLN 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 99 VAL Chi-restraints excluded: chain p residue 109 SER 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 k residue 99 THR 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 5 LEU Chi-restraints excluded: chain n residue 12 GLN Chi-restraints excluded: chain n residue 14 GLU Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain n residue 92 GLN Chi-restraints excluded: chain n residue 96 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 123 optimal weight: 0.0270 chunk 74 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 97 optimal weight: 0.0870 chunk 38 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 46 GLN g 113 GLN h 46 GLN m 32 ASN ** o 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 22 ASN k 132 ASN ** n 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11043 Z= 0.160 Angle : 0.593 9.270 14982 Z= 0.284 Chirality : 0.038 0.181 1783 Planarity : 0.003 0.035 2002 Dihedral : 4.055 56.759 1564 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.06 % Allowed : 25.33 % Favored : 70.61 % 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: 3.29 (0.24), residues: 1358 helix: 3.65 (0.19), residues: 728 sheet: -1.71 (0.40), residues: 126 loop : 1.12 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE o 109 TYR 0.019 0.001 TYR k 116 ARG 0.011 0.000 ARG o 22 *********************** 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 524 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 478 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 7 317 SER cc_start: 0.9007 (t) cc_final: 0.8638 (p) REVERT: f 123 LYS cc_start: 0.9029 (ttpt) cc_final: 0.8755 (tttt) REVERT: g 22 ASN cc_start: 0.8492 (m-40) cc_final: 0.8033 (m-40) REVERT: g 38 ASP cc_start: 0.7755 (m-30) cc_final: 0.7089 (p0) REVERT: g 123 LYS cc_start: 0.8538 (tttp) cc_final: 0.8083 (ttpp) REVERT: g 128 LYS cc_start: 0.8556 (ttmt) cc_final: 0.7996 (ttpt) REVERT: h 93 MET cc_start: 0.8635 (mmm) cc_final: 0.8330 (mmt) REVERT: h 116 ILE cc_start: 0.9288 (mm) cc_final: 0.9086 (mt) REVERT: j 82 ASN cc_start: 0.8720 (t0) cc_final: 0.8123 (t0) REVERT: j 88 ASN cc_start: 0.8490 (m110) cc_final: 0.8175 (m-40) REVERT: j 113 GLN cc_start: 0.8299 (mt0) cc_final: 0.7887 (mt0) REVERT: j 126 MET cc_start: 0.8868 (mmm) cc_final: 0.8597 (mtt) REVERT: l 12 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8104 (mm110) REVERT: l 14 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8097 (mp0) REVERT: l 17 ASN cc_start: 0.8579 (t0) cc_final: 0.8209 (t0) REVERT: l 112 ASN cc_start: 0.8796 (m110) cc_final: 0.8524 (m-40) REVERT: l 131 MET cc_start: 0.8848 (tpp) cc_final: 0.8382 (tpp) REVERT: m 4 ARG cc_start: 0.4740 (OUTLIER) cc_final: 0.4409 (mtt180) REVERT: m 21 GLN cc_start: 0.8737 (mt0) cc_final: 0.8341 (mt0) REVERT: m 23 GLN cc_start: 0.8803 (tp-100) cc_final: 0.7931 (tp40) REVERT: m 51 LYS cc_start: 0.8749 (mtpt) cc_final: 0.8523 (mtmt) REVERT: m 130 MET cc_start: 0.8909 (tpp) cc_final: 0.8577 (tpp) REVERT: o 19 ARG cc_start: 0.6995 (mmm-85) cc_final: 0.6586 (mmm160) REVERT: o 23 GLN cc_start: 0.7763 (tp40) cc_final: 0.7502 (tp40) REVERT: o 102 MET cc_start: 0.8480 (tmm) cc_final: 0.7725 (mmp) REVERT: o 104 ARG cc_start: 0.7761 (ttm-80) cc_final: 0.7438 (mtt-85) REVERT: o 107 THR cc_start: 0.9085 (m) cc_final: 0.8702 (p) REVERT: o 108 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8276 (mm-40) REVERT: o 112 ASN cc_start: 0.8383 (t0) cc_final: 0.8154 (t0) REVERT: o 115 LYS cc_start: 0.8722 (mmmm) cc_final: 0.8348 (mtmt) REVERT: p 12 SER cc_start: 0.8308 (m) cc_final: 0.7887 (p) REVERT: p 113 GLN cc_start: 0.8229 (mt0) cc_final: 0.7633 (mt0) REVERT: i 3 LEU cc_start: 0.8023 (tp) cc_final: 0.7755 (tt) REVERT: i 74 GLU cc_start: 0.7920 (pm20) cc_final: 0.7592 (pm20) REVERT: i 75 LYS cc_start: 0.8293 (mmtt) cc_final: 0.8076 (mmmt) REVERT: i 92 LYS cc_start: 0.8585 (mtpt) cc_final: 0.7984 (mtpt) REVERT: i 119 LEU cc_start: 0.9054 (tp) cc_final: 0.8836 (mt) REVERT: i 125 MET cc_start: 0.8193 (mtm) cc_final: 0.7991 (mtp) REVERT: k 10 ARG cc_start: 0.7229 (ttp80) cc_final: 0.6934 (tpt-90) REVERT: k 48 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7549 (mm-30) REVERT: k 115 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8519 (mmtp) REVERT: k 118 MET cc_start: 0.8682 (tmm) cc_final: 0.8425 (tmm) REVERT: k 130 MET cc_start: 0.8456 (tpp) cc_final: 0.8144 (tpp) outliers start: 46 outliers final: 34 residues processed: 498 average time/residue: 0.1615 time to fit residues: 111.5035 Evaluate side-chains 498 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 463 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 318 ASN Chi-restraints excluded: chain 6 residue 316 LEU Chi-restraints excluded: chain f residue 5 ASN Chi-restraints excluded: chain f residue 46 GLN Chi-restraints excluded: chain f residue 98 VAL Chi-restraints excluded: chain g residue 51 VAL Chi-restraints excluded: chain g residue 130 LEU Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 126 MET Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain j residue 127 LEU Chi-restraints excluded: chain l residue 42 ASP Chi-restraints excluded: chain l residue 54 VAL Chi-restraints excluded: chain l residue 86 LEU Chi-restraints excluded: chain l residue 114 LEU Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 4 ARG Chi-restraints excluded: chain m residue 30 ILE 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 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 99 VAL Chi-restraints excluded: chain k residue 99 THR 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 5 LEU Chi-restraints excluded: chain n residue 12 GLN Chi-restraints excluded: chain n residue 92 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: