Starting phenix.real_space_refine on Sun Aug 4 22:13:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kb5_37070/08_2024/8kb5_37070.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kb5_37070/08_2024/8kb5_37070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26133 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kb5_37070/08_2024/8kb5_37070.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kb5_37070/08_2024/8kb5_37070.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kb5_37070/08_2024/8kb5_37070.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kb5_37070/08_2024/8kb5_37070.cif" } resolution = 2.26133 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 10 5.16 5 C 6610 2.51 5 N 2249 2.21 5 O 2796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "C ARG 11": "NH1" <-> "NH2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 29": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 99": "NH1" <-> "NH2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G ARG 17": "NH1" <-> "NH2" Residue "G ARG 20": "NH1" <-> "NH2" Residue "G ARG 29": "NH1" <-> "NH2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G ARG 42": "NH1" <-> "NH2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 79": "NH1" <-> "NH2" Residue "H ARG 86": "NH1" <-> "NH2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H ARG 99": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11953 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2970 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2969 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 7.69, per 1000 atoms: 0.64 Number of scatterers: 11953 At special positions: 0 Unit cell: (117.66, 96.46, 118.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 288 15.00 O 2796 8.00 N 2249 7.00 C 6610 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: 5.98 Conformation dependent library (CDL) restraints added in 1.1 seconds 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1408 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 73.1% alpha, 2.9% beta 144 base pairs and 261 stacking pairs defined. Time for finding SS restraints: 6.10 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.148A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.685A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.501A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.705A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.766A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.349A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.871A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.125A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.673A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.032A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.071A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 412 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 261 stacking parallelities Total time for adding SS restraints: 4.65 Time building geometry restraints manager: 6.27 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: 2323 1.33 - 1.46: 4297 1.46 - 1.58: 5543 1.58 - 1.70: 577 1.70 - 1.82: 18 Bond restraints: 12758 Sorted by residual: bond pdb=" CA GLN F 93 " pdb=" C GLN F 93 " ideal model delta sigma weight residual 1.522 1.590 -0.068 1.38e-02 5.25e+03 2.43e+01 bond pdb=" CZ ARG A 134 " pdb=" NH2 ARG A 134 " ideal model delta sigma weight residual 1.330 1.281 0.049 1.30e-02 5.92e+03 1.45e+01 bond pdb=" CZ ARG G 32 " pdb=" NH2 ARG G 32 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.01e+01 bond pdb=" CZ ARG C 32 " pdb=" NH2 ARG C 32 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.01e+01 bond pdb=" CZ ARG B 95 " pdb=" NH2 ARG B 95 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.00e+01 ... (remaining 12753 not shown) Histogram of bond angle deviations from ideal: 97.40 - 104.63: 1119 104.63 - 111.86: 6825 111.86 - 119.08: 3879 119.08 - 126.31: 5757 126.31 - 133.53: 899 Bond angle restraints: 18479 Sorted by residual: angle pdb=" N GLN F 93 " pdb=" CA GLN F 93 " pdb=" C GLN F 93 " ideal model delta sigma weight residual 113.01 106.29 6.72 1.20e+00 6.94e-01 3.14e+01 angle pdb=" C ARG B 92 " pdb=" CA ARG B 92 " pdb=" CB ARG B 92 " ideal model delta sigma weight residual 110.88 103.22 7.66 1.57e+00 4.06e-01 2.38e+01 angle pdb=" N VAL F 87 " pdb=" CA VAL F 87 " pdb=" C VAL F 87 " ideal model delta sigma weight residual 110.72 105.89 4.83 1.01e+00 9.80e-01 2.28e+01 angle pdb=" C HIS A 39 " pdb=" N ARG A 40 " pdb=" CA ARG A 40 " ideal model delta sigma weight residual 120.82 127.54 -6.72 1.41e+00 5.03e-01 2.27e+01 angle pdb=" C ARG A 40 " pdb=" N TYR A 41 " pdb=" CA TYR A 41 " ideal model delta sigma weight residual 120.87 126.97 -6.10 1.42e+00 4.96e-01 1.85e+01 ... (remaining 18474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4327 17.62 - 35.24: 1141 35.24 - 52.86: 1073 52.86 - 70.48: 343 70.48 - 88.11: 16 Dihedral angle restraints: 6900 sinusoidal: 4712 harmonic: 2188 Sorted by residual: dihedral pdb=" CA PHE A 84 " pdb=" C PHE A 84 " pdb=" N GLN A 85 " pdb=" CA GLN A 85 " ideal model delta harmonic sigma weight residual 180.00 161.06 18.94 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" N GLN A 76 " pdb=" C GLN A 76 " pdb=" CA GLN A 76 " pdb=" CB GLN A 76 " ideal model delta harmonic sigma weight residual 122.80 131.80 -9.00 0 2.50e+00 1.60e-01 1.30e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 162.15 17.85 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 6897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1983 0.097 - 0.194: 111 0.194 - 0.291: 7 0.291 - 0.388: 2 0.388 - 0.485: 1 Chirality restraints: 2104 Sorted by residual: chirality pdb=" P DT I -17 " pdb=" OP1 DT I -17 " pdb=" OP2 DT I -17 " pdb=" O5' DT I -17 " both_signs ideal model delta sigma weight residual True 2.35 -2.83 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" C4' DC I 49 " pdb=" C5' DC I 49 " pdb=" O4' DC I 49 " pdb=" C3' DC I 49 " both_signs ideal model delta sigma weight residual False -2.53 -2.15 -0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA GLN A 76 " pdb=" N GLN A 76 " pdb=" C GLN A 76 " pdb=" CB GLN A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 2101 not shown) Planarity restraints: 1336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 56 " 0.119 2.00e-02 2.50e+03 6.39e-02 1.22e+02 pdb=" N9 DG J 56 " 0.033 2.00e-02 2.50e+03 pdb=" C8 DG J 56 " -0.095 2.00e-02 2.50e+03 pdb=" N7 DG J 56 " -0.092 2.00e-02 2.50e+03 pdb=" C5 DG J 56 " -0.010 2.00e-02 2.50e+03 pdb=" C6 DG J 56 " 0.041 2.00e-02 2.50e+03 pdb=" O6 DG J 56 " 0.088 2.00e-02 2.50e+03 pdb=" N1 DG J 56 " 0.030 2.00e-02 2.50e+03 pdb=" C2 DG J 56 " -0.022 2.00e-02 2.50e+03 pdb=" N2 DG J 56 " -0.069 2.00e-02 2.50e+03 pdb=" N3 DG J 56 " -0.019 2.00e-02 2.50e+03 pdb=" C4 DG J 56 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I -47 " 0.091 2.00e-02 2.50e+03 6.55e-02 1.07e+02 pdb=" N1 DT I -47 " 0.042 2.00e-02 2.50e+03 pdb=" C2 DT I -47 " -0.016 2.00e-02 2.50e+03 pdb=" O2 DT I -47 " -0.122 2.00e-02 2.50e+03 pdb=" N3 DT I -47 " 0.015 2.00e-02 2.50e+03 pdb=" C4 DT I -47 " 0.026 2.00e-02 2.50e+03 pdb=" O4 DT I -47 " 0.092 2.00e-02 2.50e+03 pdb=" C5 DT I -47 " -0.028 2.00e-02 2.50e+03 pdb=" C7 DT I -47 " -0.086 2.00e-02 2.50e+03 pdb=" C6 DT I -47 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 59 " 0.120 2.00e-02 2.50e+03 6.05e-02 1.01e+02 pdb=" N9 DA I 59 " 0.007 2.00e-02 2.50e+03 pdb=" C8 DA I 59 " -0.070 2.00e-02 2.50e+03 pdb=" N7 DA I 59 " -0.062 2.00e-02 2.50e+03 pdb=" C5 DA I 59 " -0.019 2.00e-02 2.50e+03 pdb=" C6 DA I 59 " 0.017 2.00e-02 2.50e+03 pdb=" N6 DA I 59 " 0.115 2.00e-02 2.50e+03 pdb=" N1 DA I 59 " -0.023 2.00e-02 2.50e+03 pdb=" C2 DA I 59 " -0.041 2.00e-02 2.50e+03 pdb=" N3 DA I 59 " -0.026 2.00e-02 2.50e+03 pdb=" C4 DA I 59 " -0.017 2.00e-02 2.50e+03 ... (remaining 1333 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 3664 2.88 - 3.39: 10210 3.39 - 3.89: 24290 3.89 - 4.40: 27833 4.40 - 4.90: 37547 Nonbonded interactions: 103544 Sorted by model distance: nonbonded pdb=" NE2 GLN E 125 " pdb=" OE2 GLU F 53 " model vdw 2.377 3.120 nonbonded pdb=" O ALA E 114 " pdb=" OG1 THR E 115 " model vdw 2.400 3.040 nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.457 3.040 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.488 3.040 nonbonded pdb=" OD2 ASP E 106 " pdb=" NE ARG E 131 " model vdw 2.508 3.120 ... (remaining 103539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid -72 through -1 or resid 1 through 72)) selection = (chain 'J' and (resid -72 through -1 or resid 1 through 72)) } 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 41.000 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.007 0.071 12758 Z= 0.376 Angle : 0.975 8.383 18479 Z= 0.624 Chirality : 0.049 0.485 2104 Planarity : 0.013 0.111 1336 Dihedral : 28.085 88.105 5492 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.15 (0.29), residues: 742 helix: 1.97 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -0.07 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.020 0.003 HIS E 39 PHE 0.029 0.003 PHE F 100 TYR 0.110 0.004 TYR F 51 ARG 0.012 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.914 Fit side-chains REVERT: C 61 GLU cc_start: 0.8294 (tp30) cc_final: 0.8078 (tp30) REVERT: C 99 ARG cc_start: 0.7357 (mmt180) cc_final: 0.7056 (mmm160) REVERT: D 36 SER cc_start: 0.8427 (p) cc_final: 0.8201 (p) REVERT: D 46 LYS cc_start: 0.8907 (mmpt) cc_final: 0.8586 (mmmt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 2.2302 time to fit residues: 370.9474 Evaluate side-chains 148 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 112 GLN D 63 ASN D 84 ASN F 93 GLN G 24 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12758 Z= 0.275 Angle : 0.626 8.380 18479 Z= 0.379 Chirality : 0.039 0.197 2104 Planarity : 0.005 0.043 1336 Dihedral : 30.538 74.009 4006 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.43 % Allowed : 13.54 % Favored : 85.03 % 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: 2.60 (0.30), residues: 742 helix: 2.30 (0.21), residues: 554 sheet: None (None), residues: 0 loop : 0.00 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 75 PHE 0.014 0.002 PHE E 67 TYR 0.015 0.002 TYR F 51 ARG 0.005 0.001 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 158 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: C 99 ARG cc_start: 0.7560 (mmt180) cc_final: 0.7333 (mmm160) REVERT: G 15 LYS cc_start: 0.8050 (mtpm) cc_final: 0.7738 (mtmt) outliers start: 9 outliers final: 3 residues processed: 161 average time/residue: 2.1497 time to fit residues: 362.0942 Evaluate side-chains 158 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 24 GLN C 104 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 12758 Z= 0.332 Angle : 0.664 9.213 18479 Z= 0.399 Chirality : 0.042 0.175 2104 Planarity : 0.006 0.046 1336 Dihedral : 30.671 74.333 4006 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.07 % Allowed : 13.38 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.29), residues: 742 helix: 2.19 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.06 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 75 PHE 0.014 0.002 PHE E 67 TYR 0.018 0.003 TYR H 83 ARG 0.008 0.001 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 156 time to evaluate : 0.857 Fit side-chains REVERT: C 99 ARG cc_start: 0.7619 (mmt180) cc_final: 0.7347 (mmm160) REVERT: E 59 GLU cc_start: 0.8575 (pm20) cc_final: 0.8078 (pm20) REVERT: F 79 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8730 (mtmt) REVERT: G 15 LYS cc_start: 0.8119 (mtpm) cc_final: 0.7779 (mtmt) outliers start: 13 outliers final: 8 residues processed: 160 average time/residue: 2.1447 time to fit residues: 359.2316 Evaluate side-chains 161 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12758 Z= 0.220 Angle : 0.580 7.830 18479 Z= 0.355 Chirality : 0.036 0.159 2104 Planarity : 0.005 0.044 1336 Dihedral : 30.395 73.416 4006 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.07 % Allowed : 14.65 % Favored : 83.28 % 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: 2.84 (0.30), residues: 742 helix: 2.50 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.00 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.014 0.002 PHE E 67 TYR 0.012 0.002 TYR H 83 ARG 0.008 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 0.863 Fit side-chains REVERT: C 99 ARG cc_start: 0.7498 (mmt180) cc_final: 0.7261 (mmm160) REVERT: F 79 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8724 (mtmt) REVERT: G 15 LYS cc_start: 0.8033 (mtpm) cc_final: 0.7718 (mtmt) outliers start: 13 outliers final: 4 residues processed: 159 average time/residue: 2.1263 time to fit residues: 354.3793 Evaluate side-chains 155 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 150 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12758 Z= 0.296 Angle : 0.635 8.919 18479 Z= 0.382 Chirality : 0.040 0.174 2104 Planarity : 0.005 0.044 1336 Dihedral : 30.608 73.616 4006 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.07 % Allowed : 14.17 % Favored : 83.76 % 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: 2.59 (0.30), residues: 742 helix: 2.30 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.02 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 75 PHE 0.015 0.002 PHE E 67 TYR 0.015 0.002 TYR F 51 ARG 0.005 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 157 time to evaluate : 0.826 Fit side-chains REVERT: C 99 ARG cc_start: 0.7522 (mmt180) cc_final: 0.7133 (mmm160) REVERT: E 59 GLU cc_start: 0.8489 (pm20) cc_final: 0.8010 (pm20) REVERT: E 86 ARG cc_start: 0.7580 (ttt180) cc_final: 0.7354 (tpt170) REVERT: F 79 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8724 (mtmm) REVERT: G 15 LYS cc_start: 0.8095 (mtpm) cc_final: 0.7776 (mtmt) REVERT: G 77 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7566 (mtp180) REVERT: H 105 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7365 (mm-30) outliers start: 13 outliers final: 7 residues processed: 161 average time/residue: 2.1018 time to fit residues: 354.3759 Evaluate side-chains 163 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 154 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12758 Z= 0.230 Angle : 0.609 8.389 18479 Z= 0.369 Chirality : 0.037 0.166 2104 Planarity : 0.005 0.062 1336 Dihedral : 30.600 73.568 4006 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.39 % Allowed : 14.49 % Favored : 83.12 % 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: 2.73 (0.30), residues: 742 helix: 2.42 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.05 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 129 PHE 0.014 0.002 PHE E 67 TYR 0.014 0.002 TYR F 51 ARG 0.005 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 39 HIS cc_start: 0.5859 (OUTLIER) cc_final: 0.5259 (p-80) REVERT: C 61 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7972 (tp30) REVERT: C 99 ARG cc_start: 0.7510 (mmt180) cc_final: 0.7124 (mmm160) REVERT: E 59 GLU cc_start: 0.8466 (pm20) cc_final: 0.7987 (pm20) REVERT: E 64 LYS cc_start: 0.8489 (mtpm) cc_final: 0.8202 (mppt) REVERT: E 86 ARG cc_start: 0.7531 (ttt180) cc_final: 0.7217 (tpt170) REVERT: F 79 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8720 (mtmm) REVERT: G 15 LYS cc_start: 0.8033 (mtpm) cc_final: 0.7713 (mtmt) REVERT: G 77 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7548 (mtp180) REVERT: H 105 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7332 (mm-30) outliers start: 15 outliers final: 8 residues processed: 161 average time/residue: 2.0751 time to fit residues: 350.0787 Evaluate side-chains 166 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 154 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 57 optimal weight: 0.2980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 104 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12758 Z= 0.209 Angle : 0.589 7.816 18479 Z= 0.358 Chirality : 0.036 0.162 2104 Planarity : 0.005 0.053 1336 Dihedral : 30.542 73.469 4006 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.55 % Allowed : 14.33 % Favored : 83.12 % 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: 2.81 (0.30), residues: 742 helix: 2.48 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.01 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.013 0.002 PHE E 67 TYR 0.013 0.002 TYR D 83 ARG 0.004 0.000 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 39 HIS cc_start: 0.5843 (OUTLIER) cc_final: 0.5263 (p-80) REVERT: C 61 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7960 (tp30) REVERT: C 99 ARG cc_start: 0.7502 (mmt180) cc_final: 0.7060 (mmm160) REVERT: E 86 ARG cc_start: 0.7484 (ttt180) cc_final: 0.7205 (tpt170) REVERT: F 79 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8718 (mtmt) REVERT: G 15 LYS cc_start: 0.8027 (mtpm) cc_final: 0.7710 (mtmt) REVERT: G 77 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7569 (mtp180) outliers start: 16 outliers final: 8 residues processed: 159 average time/residue: 2.1033 time to fit residues: 350.4968 Evaluate side-chains 163 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 12758 Z= 0.270 Angle : 0.614 8.547 18479 Z= 0.370 Chirality : 0.038 0.164 2104 Planarity : 0.005 0.043 1336 Dihedral : 30.523 73.171 4006 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.23 % Allowed : 14.65 % Favored : 83.12 % 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: 2.70 (0.30), residues: 742 helix: 2.40 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.04 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.014 0.002 PHE E 67 TYR 0.014 0.002 TYR F 88 ARG 0.005 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 1.125 Fit side-chains REVERT: A 39 HIS cc_start: 0.5839 (OUTLIER) cc_final: 0.5226 (p-80) REVERT: C 61 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7988 (tp30) REVERT: C 99 ARG cc_start: 0.7499 (mmt180) cc_final: 0.7123 (mmm160) REVERT: E 59 GLU cc_start: 0.8448 (pm20) cc_final: 0.7972 (pm20) REVERT: E 64 LYS cc_start: 0.8453 (mtpm) cc_final: 0.8205 (mppt) REVERT: E 86 ARG cc_start: 0.7504 (ttt180) cc_final: 0.7245 (tpt170) REVERT: F 79 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8728 (mtmt) REVERT: G 15 LYS cc_start: 0.8031 (mtpm) cc_final: 0.7712 (mtmt) REVERT: G 77 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7561 (mtp180) outliers start: 14 outliers final: 8 residues processed: 158 average time/residue: 2.2131 time to fit residues: 366.1254 Evaluate side-chains 165 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12758 Z= 0.258 Angle : 0.611 8.383 18479 Z= 0.368 Chirality : 0.038 0.168 2104 Planarity : 0.005 0.058 1336 Dihedral : 30.524 73.146 4006 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.55 % Allowed : 14.81 % Favored : 82.64 % 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: 2.71 (0.30), residues: 742 helix: 2.40 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.04 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 109 PHE 0.014 0.002 PHE E 67 TYR 0.014 0.002 TYR D 83 ARG 0.009 0.001 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 39 HIS cc_start: 0.5840 (OUTLIER) cc_final: 0.5231 (p-80) REVERT: C 99 ARG cc_start: 0.7498 (mmt180) cc_final: 0.7123 (mmm160) REVERT: E 59 GLU cc_start: 0.8447 (pm20) cc_final: 0.7971 (pm20) REVERT: E 64 LYS cc_start: 0.8445 (mtpm) cc_final: 0.8200 (mppt) REVERT: E 86 ARG cc_start: 0.7497 (ttt180) cc_final: 0.7239 (tpt170) REVERT: F 79 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8726 (mtmt) REVERT: G 15 LYS cc_start: 0.8031 (mtpm) cc_final: 0.7710 (mtmt) REVERT: G 77 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7559 (mtp180) outliers start: 16 outliers final: 9 residues processed: 160 average time/residue: 2.1485 time to fit residues: 359.9600 Evaluate side-chains 165 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.0570 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 84 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 12758 Z= 0.199 Angle : 0.601 16.367 18479 Z= 0.359 Chirality : 0.035 0.160 2104 Planarity : 0.005 0.074 1336 Dihedral : 30.513 73.369 4006 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.75 % Allowed : 15.76 % Favored : 82.48 % 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: 2.85 (0.30), residues: 742 helix: 2.51 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.01 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 109 PHE 0.014 0.001 PHE E 67 TYR 0.016 0.002 TYR H 83 ARG 0.013 0.000 ARG H 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 0.959 Fit side-chains REVERT: A 39 HIS cc_start: 0.5847 (OUTLIER) cc_final: 0.5288 (p-80) REVERT: C 99 ARG cc_start: 0.7481 (mmt180) cc_final: 0.7110 (mmm160) REVERT: E 64 LYS cc_start: 0.8447 (mtpm) cc_final: 0.8195 (mppt) REVERT: E 86 ARG cc_start: 0.7390 (ttt180) cc_final: 0.7134 (tpt170) REVERT: F 79 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8719 (mtmt) REVERT: G 15 LYS cc_start: 0.8021 (mtpm) cc_final: 0.7703 (mtmt) REVERT: G 77 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7563 (mtp180) outliers start: 11 outliers final: 6 residues processed: 155 average time/residue: 1.9829 time to fit residues: 322.0330 Evaluate side-chains 160 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 151 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 77 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 63 ASN G 24 GLN G 104 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.165856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.126164 restraints weight = 9971.700| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 0.92 r_work: 0.3241 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 12758 Z= 0.254 Angle : 0.604 8.305 18479 Z= 0.365 Chirality : 0.037 0.163 2104 Planarity : 0.005 0.049 1336 Dihedral : 30.466 72.938 4006 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.07 % Allowed : 15.92 % Favored : 82.01 % 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: 2.75 (0.30), residues: 742 helix: 2.42 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.00 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.014 0.002 PHE E 67 TYR 0.023 0.002 TYR H 83 ARG 0.007 0.001 ARG H 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5481.32 seconds wall clock time: 96 minutes 36.92 seconds (5796.92 seconds total)