Starting phenix.real_space_refine on Fri Sep 11 21:20:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xd1_33132/09_2026/7xd1_33132.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xd1_33132/09_2026/7xd1_33132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xd1_33132/09_2026/7xd1_33132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xd1_33132/09_2026/7xd1_33132.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xd1_33132/09_2026/7xd1_33132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xd1_33132/09_2026/7xd1_33132.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 294 5.49 5 S 14 5.16 5 C 6648 2.51 5 N 2268 2.21 5 O 2824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12048 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Time building chain proxies: 2.41, per 1000 atoms: 0.20 Number of scatterers: 12048 At special positions: 0 Unit cell: (119.214, 127.806, 91.29, 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 14 16.00 P 294 15.00 O 2824 8.00 N 2268 7.00 C 6648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 310.4 milliseconds 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 68.8% alpha, 3.2% beta 129 base pairs and 276 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.927A pdb=" N TYR A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.525A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.847A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.581A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.132A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.637A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.641A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.737A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.535A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.646A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.639A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.588A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.565A pdb=" N ALA E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.845A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.999A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.749A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.641A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.737A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 72 removed outlier: 3.535A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.646A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.639A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.572A pdb=" N LYS D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 84 removed outlier: 3.640A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.580A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.572A pdb=" N LYS H 46 " --> pdb=" O TYR H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 84 removed outlier: 3.640A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.580A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.907A 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 96 through 98 removed outlier: 6.597A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.291A 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 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.013A 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: 7.220A 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 78 343 hydrogen bonds defined for protein. 1017 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 317 hydrogen bonds 630 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 276 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 1.03 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: 2152 1.33 - 1.45: 4325 1.45 - 1.57: 5772 1.57 - 1.69: 588 1.69 - 1.81: 24 Bond restraints: 12861 Sorted by residual: bond pdb=" C3' DT I 15 " pdb=" C2' DT I 15 " ideal model delta sigma weight residual 1.516 1.552 -0.036 8.00e-03 1.56e+04 2.02e+01 bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.435 1.492 -0.057 1.30e-02 5.92e+03 1.91e+01 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.435 1.488 -0.053 1.30e-02 5.92e+03 1.69e+01 bond pdb=" C3' DA J -54 " pdb=" O3' DA J -54 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.35e+01 bond pdb=" C3' DT J 73 " pdb=" C2' DT J 73 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 ... (remaining 12856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 17817 2.23 - 4.46: 760 4.46 - 6.70: 33 6.70 - 8.93: 12 8.93 - 11.16: 7 Bond angle restraints: 18629 Sorted by residual: angle pdb=" CB GLU D 113 " pdb=" CG GLU D 113 " pdb=" CD GLU D 113 " ideal model delta sigma weight residual 112.60 123.17 -10.57 1.70e+00 3.46e-01 3.87e+01 angle pdb=" CB GLU H 113 " pdb=" CG GLU H 113 " pdb=" CD GLU H 113 " ideal model delta sigma weight residual 112.60 123.16 -10.56 1.70e+00 3.46e-01 3.86e+01 angle pdb=" CA GLU H 113 " pdb=" CB GLU H 113 " pdb=" CG GLU H 113 " ideal model delta sigma weight residual 114.10 125.26 -11.16 2.00e+00 2.50e-01 3.11e+01 angle pdb=" CA GLU D 113 " pdb=" CB GLU D 113 " pdb=" CG GLU D 113 " ideal model delta sigma weight residual 114.10 125.19 -11.09 2.00e+00 2.50e-01 3.08e+01 angle pdb=" C THR E 80 " pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta sigma weight residual 121.54 131.03 -9.49 1.91e+00 2.74e-01 2.47e+01 ... (remaining 18624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 5612 35.23 - 70.45: 1353 70.45 - 105.68: 8 105.68 - 140.90: 2 140.90 - 176.13: 2 Dihedral angle restraints: 6977 sinusoidal: 4775 harmonic: 2202 Sorted by residual: dihedral pdb=" CA GLU A 50 " pdb=" C GLU A 50 " pdb=" N ILE A 51 " pdb=" CA ILE A 51 " ideal model delta harmonic sigma weight residual 180.00 153.63 26.37 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA PRO E 121 " pdb=" C PRO E 121 " pdb=" N LYS E 122 " pdb=" CA LYS E 122 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual 180.00 -159.33 -20.67 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 6974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1293 0.051 - 0.102: 667 0.102 - 0.153: 141 0.153 - 0.204: 14 0.204 - 0.255: 4 Chirality restraints: 2119 Sorted by residual: chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" P DC I -58 " pdb=" OP1 DC I -58 " pdb=" OP2 DC I -58 " pdb=" O5' DC I -58 " both_signs ideal model delta sigma weight residual True 2.34 -2.56 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 2116 not shown) Planarity restraints: 1340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 88 " 0.017 2.00e-02 2.50e+03 1.83e-02 6.68e+00 pdb=" CG TYR F 88 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR F 88 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR F 88 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR F 88 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR F 88 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR F 88 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 88 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 51 " -0.016 2.00e-02 2.50e+03 1.54e-02 4.72e+00 pdb=" CG TYR B 51 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR B 51 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 51 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 51 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 51 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 51 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 51 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 25 " -0.012 2.00e-02 2.50e+03 1.46e-02 3.71e+00 pdb=" CG PHE C 25 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE C 25 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 25 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE C 25 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 25 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 25 " -0.003 2.00e-02 2.50e+03 ... (remaining 1337 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3453 2.85 - 3.37: 9714 3.37 - 3.88: 22898 3.88 - 4.39: 28712 4.39 - 4.90: 39523 Nonbonded interactions: 104300 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.343 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.344 3.040 nonbonded pdb=" NE2 GLN A 93 " pdb=" OE2 GLU A 97 " model vdw 2.345 3.120 nonbonded pdb=" O6 DG I -21 " pdb=" N4 DC J 21 " model vdw 2.381 3.120 nonbonded pdb=" O6 DG I -10 " pdb=" N4 DC J 10 " model vdw 2.391 3.120 ... (remaining 104295 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 1.360 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.400 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.010 0.080 12861 Z= 0.719 Angle : 0.993 11.158 18629 Z= 0.769 Chirality : 0.058 0.255 2119 Planarity : 0.005 0.044 1340 Dihedral : 26.766 176.131 5557 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.59 % Allowed : 3.34 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.83 (0.19), residues: 744 helix: -4.27 (0.11), residues: 524 sheet: None (None), residues: 0 loop : -2.04 (0.34), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG G 81 TYR 0.045 0.004 TYR F 88 PHE 0.033 0.004 PHE C 25 HIS 0.012 0.003 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00969 / 0.72 (12861) covalent geometry : angle 0.99326 / 0.77 (18629) hydrogen bonds : bond 0.30405 / 19.77 ( 660) hydrogen bonds : angle 10.15399 / 7.03 ( 1647) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 0.295 Fit side-chains REVERT: A 56 LYS cc_start: 0.7914 (ttpt) cc_final: 0.7632 (ttpp) REVERT: A 107 THR cc_start: 0.9122 (t) cc_final: 0.8878 (p) REVERT: A 120 MET cc_start: 0.8199 (mtm) cc_final: 0.7969 (mtp) REVERT: B 93 GLN cc_start: 0.8220 (mt0) cc_final: 0.8004 (mt0) REVERT: C 50 TYR cc_start: 0.9089 (t80) cc_final: 0.8850 (t80) REVERT: C 76 THR cc_start: 0.8500 (p) cc_final: 0.8023 (t) REVERT: E 97 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7634 (mt-10) REVERT: G 75 LYS cc_start: 0.7932 (mttm) cc_final: 0.7661 (mtmt) REVERT: D 40 TYR cc_start: 0.8764 (m-80) cc_final: 0.7998 (m-80) REVERT: D 116 LYS cc_start: 0.8499 (ttpt) cc_final: 0.8289 (mtpt) REVERT: H 37 TYR cc_start: 0.8612 (m-80) cc_final: 0.8384 (m-80) REVERT: H 120 LYS cc_start: 0.7980 (tttp) cc_final: 0.7539 (ttmm) outliers start: 10 outliers final: 0 residues processed: 189 average time/residue: 0.1636 time to fit residues: 39.2532 Evaluate side-chains 134 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 82 HIS C 84 GLN C 104 GLN E 108 ASN G 24 GLN G 82 HIS D 47 GLN H 95 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.145421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.107685 restraints weight = 15888.348| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 0.88 r_work: 0.3021 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12861 Z= 0.180 Angle : 0.784 9.841 18629 Z= 0.450 Chirality : 0.053 0.258 2119 Planarity : 0.006 0.034 1340 Dihedral : 30.706 177.004 4059 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.27 % Allowed : 7.31 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.27), residues: 744 helix: -1.37 (0.20), residues: 535 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 40 TYR 0.020 0.002 TYR B 51 PHE 0.010 0.002 PHE A 78 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.18 (12861) covalent geometry : angle 0.78445 / 0.45 (18629) hydrogen bonds : bond 0.07289 / 4.78 ( 660) hydrogen bonds : angle 3.46517 / 2.34 ( 1647) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 0.246 Fit side-chains REVERT: A 56 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7988 (ttpp) REVERT: A 120 MET cc_start: 0.8808 (mtm) cc_final: 0.8546 (mtp) REVERT: C 76 THR cc_start: 0.8654 (p) cc_final: 0.8367 (t) REVERT: G 18 SER cc_start: 0.8962 (p) cc_final: 0.8689 (m) REVERT: G 35 ARG cc_start: 0.7706 (mtm110) cc_final: 0.7391 (ttp80) REVERT: G 75 LYS cc_start: 0.8158 (mttm) cc_final: 0.7943 (mtmt) REVERT: D 36 SER cc_start: 0.9118 (p) cc_final: 0.8766 (p) REVERT: D 43 LYS cc_start: 0.8708 (mtmm) cc_final: 0.8377 (mttt) REVERT: H 34 LYS cc_start: 0.7025 (ptmm) cc_final: 0.6611 (ptmt) REVERT: H 120 LYS cc_start: 0.7990 (tttp) cc_final: 0.7625 (ttmm) outliers start: 8 outliers final: 5 residues processed: 154 average time/residue: 0.1620 time to fit residues: 32.2700 Evaluate side-chains 134 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 52 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 77 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.0050 chunk 16 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 39 HIS G 31 HIS D 109 HIS H 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.147949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.110491 restraints weight = 16105.576| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 0.88 r_work: 0.3037 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12861 Z= 0.142 Angle : 0.645 8.461 18629 Z= 0.380 Chirality : 0.047 0.284 2119 Planarity : 0.004 0.050 1340 Dihedral : 31.055 170.295 4059 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.27 % Allowed : 10.17 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.29), residues: 744 helix: 0.18 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -1.16 (0.38), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 92 TYR 0.018 0.001 TYR B 51 PHE 0.006 0.001 PHE A 67 HIS 0.006 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (12861) covalent geometry : angle 0.64525 / 0.38 (18629) hydrogen bonds : bond 0.05612 / 3.70 ( 660) hydrogen bonds : angle 2.93437 / 1.95 ( 1647) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.338 Fit side-chains REVERT: A 54 TYR cc_start: 0.8947 (m-80) cc_final: 0.8693 (m-80) REVERT: A 56 LYS cc_start: 0.8215 (ttpt) cc_final: 0.7985 (ttpp) REVERT: A 76 GLN cc_start: 0.8021 (mt0) cc_final: 0.7669 (mt0) REVERT: A 120 MET cc_start: 0.8678 (mtm) cc_final: 0.8433 (mtp) REVERT: B 79 LYS cc_start: 0.8816 (mptt) cc_final: 0.8062 (mptt) REVERT: C 76 THR cc_start: 0.8664 (p) cc_final: 0.8383 (t) REVERT: E 90 MET cc_start: 0.7780 (mmp) cc_final: 0.7379 (mmp) REVERT: D 36 SER cc_start: 0.9104 (p) cc_final: 0.8854 (p) REVERT: D 43 LYS cc_start: 0.8683 (mtmm) cc_final: 0.8399 (mttt) REVERT: D 59 MET cc_start: 0.8484 (tpp) cc_final: 0.8266 (tpp) REVERT: H 120 LYS cc_start: 0.8058 (tttp) cc_final: 0.7684 (ttmm) outliers start: 8 outliers final: 6 residues processed: 135 average time/residue: 0.1565 time to fit residues: 27.6851 Evaluate side-chains 133 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 104 GLN H 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.141584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.103763 restraints weight = 16054.491| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 0.95 r_work: 0.3012 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12861 Z= 0.163 Angle : 0.659 8.289 18629 Z= 0.377 Chirality : 0.048 0.280 2119 Planarity : 0.005 0.037 1340 Dihedral : 31.089 171.201 4059 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.11 % Allowed : 11.29 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.30), residues: 744 helix: 0.81 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -0.86 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 45 TYR 0.018 0.002 TYR B 51 PHE 0.011 0.001 PHE A 67 HIS 0.004 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 (12861) covalent geometry : angle 0.65926 / 0.38 (18629) hydrogen bonds : bond 0.05377 / 3.52 ( 660) hydrogen bonds : angle 2.80760 / 1.87 ( 1647) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.299 Fit side-chains REVERT: A 56 LYS cc_start: 0.8268 (ttpt) cc_final: 0.8009 (ttpp) REVERT: A 76 GLN cc_start: 0.8033 (mt0) cc_final: 0.7793 (mt0) REVERT: A 120 MET cc_start: 0.8654 (mtm) cc_final: 0.8404 (mtp) REVERT: B 79 LYS cc_start: 0.8802 (mptt) cc_final: 0.8008 (mptt) REVERT: C 76 THR cc_start: 0.8653 (p) cc_final: 0.8382 (t) REVERT: E 90 MET cc_start: 0.7965 (mmp) cc_final: 0.7519 (mmp) REVERT: D 36 SER cc_start: 0.9106 (p) cc_final: 0.8821 (p) REVERT: D 43 LYS cc_start: 0.8693 (mtmm) cc_final: 0.8373 (mttt) REVERT: H 120 LYS cc_start: 0.8194 (tttp) cc_final: 0.7695 (ttmm) outliers start: 7 outliers final: 5 residues processed: 136 average time/residue: 0.1576 time to fit residues: 27.9770 Evaluate side-chains 136 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 55 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 96 optimal weight: 0.0980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN C 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.141777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.103657 restraints weight = 16141.392| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 0.90 r_work: 0.2995 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12861 Z= 0.192 Angle : 0.685 8.321 18629 Z= 0.386 Chirality : 0.049 0.282 2119 Planarity : 0.005 0.042 1340 Dihedral : 31.230 171.707 4059 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.59 % Allowed : 12.56 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.30), residues: 744 helix: 1.03 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -0.96 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 49 TYR 0.019 0.002 TYR B 51 PHE 0.009 0.002 PHE A 67 HIS 0.006 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (12861) covalent geometry : angle 0.68522 / 0.39 (18629) hydrogen bonds : bond 0.05598 / 3.68 ( 660) hydrogen bonds : angle 2.82411 / 1.88 ( 1647) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.324 Fit side-chains REVERT: A 56 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8190 (ttpp) REVERT: A 76 GLN cc_start: 0.8034 (mt0) cc_final: 0.7716 (mt0) REVERT: A 120 MET cc_start: 0.8604 (mtm) cc_final: 0.8374 (mtp) REVERT: B 79 LYS cc_start: 0.8814 (mptt) cc_final: 0.7997 (mptt) REVERT: C 76 THR cc_start: 0.8633 (p) cc_final: 0.8348 (t) REVERT: E 90 MET cc_start: 0.8036 (mmp) cc_final: 0.7591 (mmp) REVERT: D 36 SER cc_start: 0.9136 (p) cc_final: 0.8864 (p) REVERT: D 43 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8333 (mttt) REVERT: H 120 LYS cc_start: 0.8150 (tttp) cc_final: 0.7630 (ttmm) outliers start: 10 outliers final: 8 residues processed: 141 average time/residue: 0.1574 time to fit residues: 28.7525 Evaluate side-chains 141 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 30 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 45 optimal weight: 0.0570 chunk 22 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN C 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.142080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.104123 restraints weight = 16223.672| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 0.95 r_work: 0.2995 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12861 Z= 0.139 Angle : 0.639 7.908 18629 Z= 0.369 Chirality : 0.047 0.272 2119 Planarity : 0.004 0.036 1340 Dihedral : 31.120 170.754 4059 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.43 % Allowed : 11.76 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.31), residues: 744 helix: 1.36 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -0.81 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 131 TYR 0.014 0.001 TYR B 51 PHE 0.007 0.001 PHE A 67 HIS 0.006 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (12861) covalent geometry : angle 0.63922 / 0.37 (18629) hydrogen bonds : bond 0.05068 / 3.31 ( 660) hydrogen bonds : angle 2.76275 / 1.83 ( 1647) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.267 Fit side-chains REVERT: A 56 LYS cc_start: 0.8440 (ttpt) cc_final: 0.8228 (ttpp) REVERT: A 76 GLN cc_start: 0.8147 (mt0) cc_final: 0.7808 (mt0) REVERT: A 120 MET cc_start: 0.8618 (mtm) cc_final: 0.8370 (mtp) REVERT: B 59 LYS cc_start: 0.8714 (tptt) cc_final: 0.8252 (tppt) REVERT: C 76 THR cc_start: 0.8628 (p) cc_final: 0.8357 (t) REVERT: E 90 MET cc_start: 0.7995 (mmp) cc_final: 0.7581 (mmp) REVERT: D 36 SER cc_start: 0.9123 (p) cc_final: 0.8850 (p) REVERT: D 43 LYS cc_start: 0.8655 (mtmm) cc_final: 0.8329 (mttt) REVERT: H 120 LYS cc_start: 0.8191 (tttp) cc_final: 0.7675 (ttmm) outliers start: 9 outliers final: 7 residues processed: 137 average time/residue: 0.1510 time to fit residues: 27.0004 Evaluate side-chains 140 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 133 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.106475 restraints weight = 16063.446| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 0.89 r_work: 0.3020 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12861 Z= 0.145 Angle : 0.617 8.047 18629 Z= 0.359 Chirality : 0.045 0.277 2119 Planarity : 0.004 0.036 1340 Dihedral : 30.987 169.334 4059 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.07 % Allowed : 12.24 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.31), residues: 744 helix: 1.64 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -0.77 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 36 TYR 0.014 0.001 TYR B 51 PHE 0.006 0.001 PHE A 67 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (12861) covalent geometry : angle 0.61744 / 0.36 (18629) hydrogen bonds : bond 0.04972 / 3.23 ( 660) hydrogen bonds : angle 2.68836 / 1.78 ( 1647) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.215 Fit side-chains REVERT: A 56 LYS cc_start: 0.8425 (ttpt) cc_final: 0.8216 (ttpp) REVERT: A 76 GLN cc_start: 0.8068 (mt0) cc_final: 0.7700 (mt0) REVERT: A 97 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: A 120 MET cc_start: 0.8592 (mtm) cc_final: 0.8343 (mtp) REVERT: B 59 LYS cc_start: 0.8684 (tptt) cc_final: 0.8286 (tppt) REVERT: C 76 THR cc_start: 0.8602 (p) cc_final: 0.8337 (t) REVERT: E 90 MET cc_start: 0.8041 (mmp) cc_final: 0.7611 (mmp) REVERT: G 61 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8141 (tp30) REVERT: D 36 SER cc_start: 0.9119 (p) cc_final: 0.8829 (p) REVERT: D 43 LYS cc_start: 0.8640 (mtmm) cc_final: 0.8299 (mttt) REVERT: H 120 LYS cc_start: 0.8167 (tttp) cc_final: 0.7644 (ttmm) outliers start: 13 outliers final: 7 residues processed: 139 average time/residue: 0.1658 time to fit residues: 29.6900 Evaluate side-chains 139 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.143606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.105752 restraints weight = 16037.564| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 0.89 r_work: 0.3030 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12861 Z= 0.147 Angle : 0.616 8.025 18629 Z= 0.357 Chirality : 0.045 0.274 2119 Planarity : 0.004 0.037 1340 Dihedral : 30.971 169.680 4059 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.59 % Allowed : 13.04 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.31), residues: 744 helix: 1.74 (0.23), residues: 531 sheet: None (None), residues: 0 loop : -0.72 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 36 TYR 0.012 0.001 TYR A 54 PHE 0.007 0.001 PHE A 67 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (12861) covalent geometry : angle 0.61561 / 0.36 (18629) hydrogen bonds : bond 0.04916 / 3.20 ( 660) hydrogen bonds : angle 2.67001 / 1.76 ( 1647) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.207 Fit side-chains REVERT: A 56 LYS cc_start: 0.8437 (ttpt) cc_final: 0.8230 (ttpp) REVERT: A 76 GLN cc_start: 0.8065 (mt0) cc_final: 0.7683 (mt0) REVERT: A 97 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: A 120 MET cc_start: 0.8577 (mtm) cc_final: 0.8335 (mtp) REVERT: C 76 THR cc_start: 0.8582 (p) cc_final: 0.8322 (t) REVERT: E 90 MET cc_start: 0.8024 (mmp) cc_final: 0.7593 (mmp) REVERT: E 129 ARG cc_start: 0.8208 (tpt90) cc_final: 0.7561 (ttt90) REVERT: G 61 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8149 (tp30) REVERT: D 36 SER cc_start: 0.9114 (p) cc_final: 0.8829 (p) REVERT: D 43 LYS cc_start: 0.8658 (mtmm) cc_final: 0.8331 (mttt) REVERT: H 120 LYS cc_start: 0.8149 (tttp) cc_final: 0.7631 (ttmm) outliers start: 10 outliers final: 8 residues processed: 139 average time/residue: 0.1676 time to fit residues: 30.0471 Evaluate side-chains 142 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 18 optimal weight: 0.0980 chunk 23 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.138369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.100003 restraints weight = 16038.224| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 0.94 r_work: 0.2938 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 12861 Z= 0.277 Angle : 0.773 8.909 18629 Z= 0.420 Chirality : 0.055 0.284 2119 Planarity : 0.007 0.058 1340 Dihedral : 31.453 173.558 4059 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.91 % Allowed : 13.20 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.30), residues: 744 helix: 1.06 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.08 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 40 TYR 0.017 0.002 TYR B 51 PHE 0.010 0.002 PHE A 67 HIS 0.008 0.002 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.28 (12861) covalent geometry : angle 0.77338 / 0.42 (18629) hydrogen bonds : bond 0.06384 / 4.20 ( 660) hydrogen bonds : angle 2.97865 / 2.00 ( 1647) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.317 Fit side-chains REVERT: A 56 LYS cc_start: 0.8486 (ttpt) cc_final: 0.8229 (ttpp) REVERT: A 76 GLN cc_start: 0.8081 (mt0) cc_final: 0.7805 (mt0) REVERT: A 97 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: A 120 MET cc_start: 0.8658 (mtm) cc_final: 0.8428 (mtp) REVERT: C 76 THR cc_start: 0.8682 (p) cc_final: 0.8334 (t) REVERT: G 61 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8310 (tp30) REVERT: D 43 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8381 (mttt) outliers start: 12 outliers final: 9 residues processed: 131 average time/residue: 0.1647 time to fit residues: 28.1756 Evaluate side-chains 131 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 68 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.141479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.103300 restraints weight = 16069.139| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 0.91 r_work: 0.2971 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12861 Z= 0.162 Angle : 0.682 7.792 18629 Z= 0.384 Chirality : 0.049 0.270 2119 Planarity : 0.005 0.038 1340 Dihedral : 31.349 172.212 4059 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.43 % Allowed : 13.99 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.30), residues: 744 helix: 1.30 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -0.95 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 55 TYR 0.015 0.002 TYR B 51 PHE 0.007 0.001 PHE A 67 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (12861) covalent geometry : angle 0.68189 / 0.38 (18629) hydrogen bonds : bond 0.05442 / 3.55 ( 660) hydrogen bonds : angle 2.85495 / 1.90 ( 1647) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.287 Fit side-chains REVERT: A 42 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7783 (mtm-85) REVERT: A 56 LYS cc_start: 0.8466 (ttpt) cc_final: 0.8211 (ttpp) REVERT: A 76 GLN cc_start: 0.8058 (mt0) cc_final: 0.7767 (mt0) REVERT: A 97 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: A 120 MET cc_start: 0.8598 (mtm) cc_final: 0.8362 (mtp) REVERT: C 76 THR cc_start: 0.8621 (p) cc_final: 0.8340 (t) REVERT: G 61 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8223 (tp30) REVERT: D 36 SER cc_start: 0.9128 (p) cc_final: 0.8860 (p) REVERT: D 43 LYS cc_start: 0.8663 (mtmm) cc_final: 0.8318 (mttt) REVERT: H 120 LYS cc_start: 0.8130 (tttp) cc_final: 0.7615 (ttmm) outliers start: 9 outliers final: 7 residues processed: 136 average time/residue: 0.1647 time to fit residues: 29.1432 Evaluate side-chains 138 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 86 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 18 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 55 optimal weight: 9.9990 chunk 96 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN C 104 GLN H 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.141071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.102921 restraints weight = 15990.190| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 0.94 r_work: 0.2962 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12861 Z= 0.150 Angle : 0.655 7.415 18629 Z= 0.372 Chirality : 0.047 0.269 2119 Planarity : 0.004 0.037 1340 Dihedral : 31.224 171.042 4059 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.75 % Allowed : 13.99 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.30), residues: 744 helix: 1.56 (0.23), residues: 531 sheet: None (None), residues: 0 loop : -0.84 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 36 TYR 0.011 0.001 TYR A 54 PHE 0.007 0.001 PHE H 70 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (12861) covalent geometry : angle 0.65462 / 0.37 (18629) hydrogen bonds : bond 0.05145 / 3.35 ( 660) hydrogen bonds : angle 2.80841 / 1.85 ( 1647) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2755.68 seconds wall clock time: 47 minutes 45.87 seconds (2865.87 seconds total)