Starting phenix.real_space_refine on Sat Jul 4 18:20:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r5w_53596/07_2026/9r5w_53596.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r5w_53596/07_2026/9r5w_53596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r5w_53596/07_2026/9r5w_53596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r5w_53596/07_2026/9r5w_53596.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r5w_53596/07_2026/9r5w_53596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r5w_53596/07_2026/9r5w_53596.map" } resolution = 3.8 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= 0.001 sd= 0.028 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: 6 Type Number sf(0) Gaussians P 323 5.49 5 S 10 5.16 5 C 6835 2.51 5 N 2340 2.21 5 O 2983 1.98 5 H 9763 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22254 Number of models: 1 Model: "" Number of chains: 10 Chain: "I" Number of atoms: 5129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 5129 Classifications: {'DNA': 162} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 161} Chain: "J" Number of atoms: 5146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 5146 Classifications: {'DNA': 162} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 161} Chain: "A" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1622 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1314 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1642 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1492 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1620 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1298 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} 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: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1537 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "H" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1454 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.91, per 1000 atoms: 0.13 Number of scatterers: 22254 At special positions: 0 Unit cell: (77.55, 151.25, 132.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 P 323 15.00 O 2983 8.00 N 2340 7.00 C 6835 6.00 H 9763 1.00 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: 1.73 Conformation dependent library (CDL) restraints added in 391.2 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1378 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 9 sheets defined 73.0% alpha, 2.7% beta 158 base pairs and 256 stacking pairs defined. Time for finding SS restraints: 4.15 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.136A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.664A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.863A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.881A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.868A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.580A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.572A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.970A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.984A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.606A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.708A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 98 Processing helix chain 'D' and resid 102 through 120 removed outlier: 3.643A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 removed outlier: 3.605A pdb=" N GLU E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.527A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.797A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.858A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.569A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY F 42 " --> pdb=" O ALA F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.996A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.508A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.635A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.630A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.882A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.619A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.535A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 removed outlier: 4.038A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.368A 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 removed outlier: 3.511A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.307A 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: 6.982A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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 101 through 102 removed outlier: 7.207A 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: 7.097A 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: 6.905A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 358 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 406 hydrogen bonds 812 hydrogen bond angles 0 basepair planarities 158 basepair parallelities 256 stacking parallelities Total time for adding SS restraints: 5.00 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9763 1.03 - 1.22: 70 1.22 - 1.42: 5553 1.42 - 1.61: 7726 1.61 - 1.80: 28 Bond restraints: 23140 Sorted by residual: bond pdb=" N3 DC I 19 " pdb=" C4 DC I 19 " ideal model delta sigma weight residual 1.335 1.306 0.029 7.00e-03 2.04e+04 1.75e+01 bond pdb=" C1' DC I 7 " pdb=" N1 DC I 7 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.24e+01 bond pdb=" C1' DC J 34 " pdb=" N1 DC J 34 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.20e+01 bond pdb=" C1' DC J -58 " pdb=" N1 DC J -58 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.15e+01 bond pdb=" C1' DC I 6 " pdb=" N1 DC I 6 " ideal model delta sigma weight residual 1.468 1.512 -0.044 1.40e-02 5.10e+03 1.00e+01 ... (remaining 23135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 40546 2.11 - 4.22: 1367 4.22 - 6.33: 14 6.33 - 8.43: 2 8.43 - 10.54: 4 Bond angle restraints: 41933 Sorted by residual: angle pdb=" N3 DT J 74 " pdb=" C4 DT J 74 " pdb=" O4 DT J 74 " ideal model delta sigma weight residual 119.90 123.11 -3.21 6.00e-01 2.78e+00 2.86e+01 angle pdb=" N3 DT J 84 " pdb=" C4 DT J 84 " pdb=" O4 DT J 84 " ideal model delta sigma weight residual 119.90 122.80 -2.90 6.00e-01 2.78e+00 2.34e+01 angle pdb=" O4 DT J 74 " pdb=" C4 DT J 74 " pdb=" C5 DT J 74 " ideal model delta sigma weight residual 124.90 121.56 3.34 7.00e-01 2.04e+00 2.27e+01 angle pdb=" N3 DT J -71 " pdb=" C4 DT J -71 " pdb=" O4 DT J -71 " ideal model delta sigma weight residual 119.90 122.67 -2.77 6.00e-01 2.78e+00 2.13e+01 angle pdb=" O4' DC J 76 " pdb=" C1' DC J 76 " pdb=" N1 DC J 76 " ideal model delta sigma weight residual 108.00 111.19 -3.19 7.00e-01 2.04e+00 2.07e+01 ... (remaining 41928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 6622 17.20 - 34.39: 1191 34.39 - 51.59: 1212 51.59 - 68.78: 488 68.78 - 85.98: 11 Dihedral angle restraints: 9524 sinusoidal: 7124 harmonic: 2400 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 161.03 18.97 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ARG E 63 " pdb=" C ARG E 63 " pdb=" N LYS E 64 " pdb=" CA LYS E 64 " ideal model delta harmonic sigma weight residual -180.00 -161.92 -18.08 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA PRO H 47 " pdb=" C PRO H 47 " pdb=" N ASP H 48 " pdb=" CA ASP H 48 " ideal model delta harmonic sigma weight residual 180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 9521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1853 0.085 - 0.171: 353 0.171 - 0.256: 4 0.256 - 0.341: 0 0.341 - 0.426: 2 Chirality restraints: 2212 Sorted by residual: chirality pdb=" P DT I -72 " pdb=" OP1 DT I -72 " pdb=" OP2 DT I -72 " pdb=" O5' DT I -72 " both_signs ideal model delta sigma weight residual True 2.34 -2.76 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" P DC I -73 " pdb=" OP1 DC I -73 " pdb=" OP2 DC I -73 " pdb=" O5' DC I -73 " both_signs ideal model delta sigma weight residual True 2.34 -2.74 -0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" P DC J -20 " pdb=" OP1 DC J -20 " pdb=" OP2 DC J -20 " pdb=" O5' DC J -20 " both_signs ideal model delta sigma weight residual True 2.34 -2.54 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 2209 not shown) Planarity restraints: 2310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J -20 " 0.003 2.00e-02 2.50e+03 2.32e-02 1.48e+01 pdb=" N1 DC J -20 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DC J -20 " 0.061 2.00e-02 2.50e+03 pdb=" O2 DC J -20 " -0.038 2.00e-02 2.50e+03 pdb=" N3 DC J -20 " -0.018 2.00e-02 2.50e+03 pdb=" C4 DC J -20 " 0.017 2.00e-02 2.50e+03 pdb=" N4 DC J -20 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DC J -20 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC J -20 " -0.001 2.00e-02 2.50e+03 pdb=" H5 DC J -20 " -0.006 2.00e-02 2.50e+03 pdb=" H6 DC J -20 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 19 " -0.017 2.00e-02 2.50e+03 1.73e-02 8.23e+00 pdb=" N1 DC I 19 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DC I 19 " -0.036 2.00e-02 2.50e+03 pdb=" O2 DC I 19 " 0.038 2.00e-02 2.50e+03 pdb=" N3 DC I 19 " -0.011 2.00e-02 2.50e+03 pdb=" C4 DC I 19 " 0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 19 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DC I 19 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DC I 19 " 0.004 2.00e-02 2.50e+03 pdb=" H5 DC I 19 " 0.006 2.00e-02 2.50e+03 pdb=" H6 DC I 19 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU H 103 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" C LEU H 103 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU H 103 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA H 104 " -0.015 2.00e-02 2.50e+03 ... (remaining 2307 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 853 2.19 - 2.79: 36865 2.79 - 3.40: 54052 3.40 - 4.00: 75698 4.00 - 4.60: 113984 Nonbonded interactions: 281452 Sorted by model distance: nonbonded pdb=" HZ PHE E 104 " pdb=" HG1 THR F 54 " model vdw 1.589 2.100 nonbonded pdb=" OD1 ASN G 68 " pdb="HH21 ARG G 71 " model vdw 1.640 2.450 nonbonded pdb=" O ILE D 36 " pdb=" HZ3 LYS D 40 " model vdw 1.688 2.450 nonbonded pdb=" OE2 GLU G 64 " pdb="HD21 ASN G 68 " model vdw 1.699 2.450 nonbonded pdb=" OP1 DA I -44 " pdb="HH12 ARG C 32 " model vdw 1.709 2.450 ... (remaining 281447 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 39 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name HA or name HB \ 2 or name HB3)) or resid 40 through 133 or (resid 134 and (name N or name CA or \ name C or name O or name CB or name H or name HA )))) selection = (chain 'E' and ((resid 39 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name HA or name HB \ 2 or name HB3)) or resid 40 through 134)) } ncs_group { reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name HA )) or resid 24 through 102)) selection = (chain 'F' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name HA )) or resid 24 through 102)) } ncs_group { reference = (chain 'C' and resid 14 through 109) selection = (chain 'G' and resid 14 through 109) } ncs_group { reference = (chain 'D' and ((resid 30 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ E or name HH11 or name HH12 or name HH21 or name HH22)) or resid 31 through 120 \ or (resid 121 and (name N or name CA or name C or name O or name H )))) 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 group one per residue 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: 16.020 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: 0.140 Extract box with map and model: 0.540 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.650 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 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 : 0.006 0.049 13377 Z= 0.568 Angle : 0.866 10.543 19463 Z= 0.753 Chirality : 0.059 0.426 2212 Planarity : 0.006 0.049 1343 Dihedral : 26.919 82.580 5801 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.34 % Favored : 97.52 % Rotamer: Outliers : 0.16 % Allowed : 0.33 % Favored : 99.51 % 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: 1.41 (0.29), residues: 726 helix: 1.70 (0.23), residues: 460 sheet: None (None), residues: 0 loop : -0.38 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 96 TYR 0.011 0.001 TYR A 99 PHE 0.012 0.001 PHE B 61 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.57 (13377) covalent geometry : angle 0.86562 / 0.75 (19463) hydrogen bonds : bond 0.14914 / 16.60 ( 764) hydrogen bonds : angle 4.97391 / 6.48 ( 1880) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 TYR cc_start: 0.6589 (m-80) cc_final: 0.6367 (m-80) REVERT: B 91 LYS cc_start: 0.8099 (ttmt) cc_final: 0.7825 (ttmm) REVERT: E 42 ARG cc_start: 0.7880 (mtp180) cc_final: 0.7547 (mtp85) REVERT: G 13 LYS cc_start: 0.7890 (tptp) cc_final: 0.7679 (tptp) outliers start: 1 outliers final: 0 residues processed: 91 average time/residue: 0.3915 time to fit residues: 44.8647 Evaluate side-chains 84 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.144432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120790 restraints weight = 49868.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.123934 restraints weight = 18157.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 78)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.125983 restraints weight = 9486.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127145 restraints weight = 6522.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.128035 restraints weight = 5290.199| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13377 Z= 0.213 Angle : 0.702 6.201 19463 Z= 0.448 Chirality : 0.047 0.171 2212 Planarity : 0.005 0.064 1343 Dihedral : 30.112 75.987 4361 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.82 % Allowed : 5.43 % Favored : 93.75 % 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: 1.73 (0.30), residues: 726 helix: 1.99 (0.23), residues: 487 sheet: None (None), residues: 0 loop : -0.63 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 55 TYR 0.012 0.001 TYR H 39 PHE 0.011 0.001 PHE B 61 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.21 (13377) covalent geometry : angle 0.70222 / 0.45 (19463) hydrogen bonds : bond 0.07952 / 8.96 ( 764) hydrogen bonds : angle 3.69235 / 4.79 ( 1880) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.6430 (OUTLIER) cc_final: 0.6155 (mpp) REVERT: G 38 ASN cc_start: 0.7975 (m-40) cc_final: 0.7752 (m-40) outliers start: 5 outliers final: 4 residues processed: 85 average time/residue: 0.3676 time to fit residues: 39.8294 Evaluate side-chains 89 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain H residue 32 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 94 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 74 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 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 = 0.3832 r_free = 0.3832 target = 0.142691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118642 restraints weight = 49874.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.121771 restraints weight = 18394.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.123875 restraints weight = 9797.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.125036 restraints weight = 6771.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.125874 restraints weight = 5531.395| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13377 Z= 0.192 Angle : 0.619 6.854 19463 Z= 0.418 Chirality : 0.041 0.221 2212 Planarity : 0.004 0.047 1343 Dihedral : 30.134 76.198 4361 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.15 % Allowed : 5.92 % Favored : 92.93 % 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: 1.97 (0.31), residues: 726 helix: 2.32 (0.23), residues: 491 sheet: None (None), residues: 0 loop : -0.97 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 42 TYR 0.008 0.001 TYR A 41 PHE 0.007 0.001 PHE B 61 HIS 0.007 0.002 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.19 (13377) covalent geometry : angle 0.61902 / 0.42 (19463) hydrogen bonds : bond 0.07310 / 8.28 ( 764) hydrogen bonds : angle 3.32317 / 4.33 ( 1880) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 92 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7902 (ttp80) REVERT: G 73 ASN cc_start: 0.8494 (t0) cc_final: 0.8215 (t0) outliers start: 7 outliers final: 3 residues processed: 91 average time/residue: 0.3570 time to fit residues: 41.4759 Evaluate side-chains 88 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 90 optimal weight: 0.9980 chunk 99 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.139425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.114559 restraints weight = 49684.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117930 restraints weight = 17631.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.119841 restraints weight = 9128.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 75)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.121337 restraints weight = 6329.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.122034 restraints weight = 5108.240| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13377 Z= 0.212 Angle : 0.657 6.832 19463 Z= 0.418 Chirality : 0.043 0.164 2212 Planarity : 0.004 0.042 1343 Dihedral : 30.099 73.895 4361 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.15 % Allowed : 7.07 % Favored : 91.78 % 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: 2.10 (0.31), residues: 726 helix: 2.47 (0.23), residues: 489 sheet: None (None), residues: 0 loop : -1.01 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.010 0.001 TYR D 37 PHE 0.010 0.001 PHE B 61 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.21 (13377) covalent geometry : angle 0.65727 / 0.42 (19463) hydrogen bonds : bond 0.07553 / 8.48 ( 764) hydrogen bonds : angle 3.25334 / 4.21 ( 1880) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 75 HIS cc_start: 0.7890 (t70) cc_final: 0.7363 (t70) REVERT: F 92 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7949 (ttp80) outliers start: 7 outliers final: 5 residues processed: 87 average time/residue: 0.3648 time to fit residues: 40.4013 Evaluate side-chains 89 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 82 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 13 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 110 ASN ** 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 = 0.3467 r_free = 0.3467 target = 0.118087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.094598 restraints weight = 48292.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.097463 restraints weight = 17555.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.099154 restraints weight = 9171.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100251 restraints weight = 6310.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.100971 restraints weight = 5090.815| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13377 Z= 0.192 Angle : 0.597 6.211 19463 Z= 0.397 Chirality : 0.040 0.144 2212 Planarity : 0.004 0.040 1343 Dihedral : 30.074 74.371 4361 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.48 % Allowed : 7.40 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.18 (0.31), residues: 726 helix: 2.54 (0.23), residues: 489 sheet: None (None), residues: 0 loop : -1.02 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.019 0.001 TYR D 118 PHE 0.009 0.001 PHE B 61 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.19 (13377) covalent geometry : angle 0.59693 / 0.40 (19463) hydrogen bonds : bond 0.07150 / 8.08 ( 764) hydrogen bonds : angle 3.15959 / 4.09 ( 1880) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 92 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7956 (ttp80) outliers start: 9 outliers final: 6 residues processed: 89 average time/residue: 0.3728 time to fit residues: 41.8622 Evaluate side-chains 90 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 22 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 101 optimal weight: 0.0470 chunk 84 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.138399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.113249 restraints weight = 49044.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.116624 restraints weight = 17397.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.118816 restraints weight = 9017.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120013 restraints weight = 6166.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.120916 restraints weight = 5020.835| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13377 Z= 0.178 Angle : 0.586 6.309 19463 Z= 0.387 Chirality : 0.039 0.142 2212 Planarity : 0.004 0.040 1343 Dihedral : 30.042 74.791 4361 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.32 % Allowed : 7.40 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.31), residues: 726 helix: 2.68 (0.23), residues: 489 sheet: None (None), residues: 0 loop : -0.99 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 42 TYR 0.011 0.001 TYR D 118 PHE 0.008 0.001 PHE B 61 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.18 (13377) covalent geometry : angle 0.58623 / 0.39 (19463) hydrogen bonds : bond 0.06757 / 7.61 ( 764) hydrogen bonds : angle 3.05788 / 3.96 ( 1880) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 92 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7976 (ttp80) REVERT: H 45 VAL cc_start: 0.7839 (t) cc_final: 0.7545 (t) outliers start: 8 outliers final: 5 residues processed: 87 average time/residue: 0.3958 time to fit residues: 43.4565 Evaluate side-chains 91 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 40 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.135817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.110280 restraints weight = 48707.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.113647 restraints weight = 17405.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.115840 restraints weight = 9093.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.117037 restraints weight = 6254.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.117901 restraints weight = 5108.404| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13377 Z= 0.217 Angle : 0.625 7.084 19463 Z= 0.405 Chirality : 0.040 0.159 2212 Planarity : 0.005 0.060 1343 Dihedral : 29.985 74.397 4361 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.82 % Allowed : 9.05 % Favored : 90.13 % 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: 2.13 (0.31), residues: 726 helix: 2.52 (0.23), residues: 489 sheet: None (None), residues: 0 loop : -1.06 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.026 0.002 TYR H 118 PHE 0.009 0.001 PHE B 61 HIS 0.009 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.22 (13377) covalent geometry : angle 0.62539 / 0.40 (19463) hydrogen bonds : bond 0.07561 / 8.52 ( 764) hydrogen bonds : angle 3.17491 / 4.10 ( 1880) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 75 HIS cc_start: 0.7952 (t70) cc_final: 0.7405 (t70) REVERT: F 92 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8013 (ttp80) outliers start: 5 outliers final: 3 residues processed: 89 average time/residue: 0.3834 time to fit residues: 43.1159 Evaluate side-chains 91 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 0.1980 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.130517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.104961 restraints weight = 47879.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.108168 restraints weight = 16857.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.110243 restraints weight = 8826.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.111499 restraints weight = 6115.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.112158 restraints weight = 4991.173| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13377 Z= 0.309 Angle : 0.712 8.208 19463 Z= 0.447 Chirality : 0.044 0.192 2212 Planarity : 0.006 0.047 1343 Dihedral : 30.009 76.456 4361 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.81 % Allowed : 9.05 % Favored : 89.14 % 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: 1.41 (0.30), residues: 726 helix: 1.96 (0.22), residues: 501 sheet: None (None), residues: 0 loop : -1.51 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 42 TYR 0.026 0.003 TYR D 118 PHE 0.012 0.002 PHE E 67 HIS 0.009 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.31 (13377) covalent geometry : angle 0.71230 / 0.45 (19463) hydrogen bonds : bond 0.09133 / 10.27 ( 764) hydrogen bonds : angle 3.54063 / 4.55 ( 1880) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 27 GLN cc_start: 0.8320 (mm-40) cc_final: 0.7797 (mp10) REVERT: F 92 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8062 (ttp80) REVERT: H 117 LYS cc_start: 0.8746 (tttp) cc_final: 0.8505 (tttp) outliers start: 11 outliers final: 5 residues processed: 93 average time/residue: 0.4096 time to fit residues: 47.5536 Evaluate side-chains 92 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 48 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.134880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109103 restraints weight = 48196.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.112399 restraints weight = 17237.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.114548 restraints weight = 9092.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.115748 restraints weight = 6314.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.116597 restraints weight = 5169.723| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13377 Z= 0.193 Angle : 0.616 6.697 19463 Z= 0.404 Chirality : 0.040 0.155 2212 Planarity : 0.005 0.049 1343 Dihedral : 29.955 76.622 4361 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.32 % Allowed : 9.54 % Favored : 89.14 % 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: 1.73 (0.31), residues: 726 helix: 2.23 (0.23), residues: 489 sheet: None (None), residues: 0 loop : -1.26 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 42 TYR 0.016 0.002 TYR D 118 PHE 0.008 0.001 PHE G 25 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.19 (13377) covalent geometry : angle 0.61603 / 0.40 (19463) hydrogen bonds : bond 0.07811 / 8.84 ( 764) hydrogen bonds : angle 3.25888 / 4.20 ( 1880) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8564 (mtm180) cc_final: 0.8260 (mtm180) REVERT: F 27 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7730 (mp10) REVERT: F 92 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8063 (ttp80) REVERT: H 117 LYS cc_start: 0.8792 (tttp) cc_final: 0.8543 (tttp) outliers start: 8 outliers final: 6 residues processed: 91 average time/residue: 0.3923 time to fit residues: 45.0105 Evaluate side-chains 93 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 69 optimal weight: 0.0670 chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 0.2980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.135756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.109885 restraints weight = 48404.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113204 restraints weight = 17128.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.115352 restraints weight = 9011.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.116648 restraints weight = 6251.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.117373 restraints weight = 5097.079| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13377 Z= 0.188 Angle : 0.602 10.561 19463 Z= 0.393 Chirality : 0.039 0.145 2212 Planarity : 0.005 0.046 1343 Dihedral : 29.876 77.238 4361 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.32 % Allowed : 10.03 % Favored : 88.65 % 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: 2.06 (0.31), residues: 726 helix: 2.48 (0.23), residues: 489 sheet: None (None), residues: 0 loop : -1.14 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 42 TYR 0.015 0.001 TYR D 118 PHE 0.008 0.001 PHE B 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.19 (13377) covalent geometry : angle 0.60153 / 0.39 (19463) hydrogen bonds : bond 0.07029 / 7.92 ( 764) hydrogen bonds : angle 3.11273 / 4.00 ( 1880) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 27 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7849 (mp10) REVERT: F 92 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8040 (ttp80) REVERT: H 117 LYS cc_start: 0.8770 (tttp) cc_final: 0.8530 (tttp) outliers start: 8 outliers final: 5 residues processed: 88 average time/residue: 0.3941 time to fit residues: 44.0313 Evaluate side-chains 88 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 92 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 1 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 81 optimal weight: 0.0970 chunk 90 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.134189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.108553 restraints weight = 47880.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.111828 restraints weight = 16794.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.113724 restraints weight = 8787.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.115231 restraints weight = 6163.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.115843 restraints weight = 4980.299| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13377 Z= 0.197 Angle : 0.600 6.831 19463 Z= 0.392 Chirality : 0.039 0.151 2212 Planarity : 0.004 0.044 1343 Dihedral : 29.845 78.003 4361 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.15 % Allowed : 10.53 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.31), residues: 726 helix: 2.49 (0.23), residues: 489 sheet: None (None), residues: 0 loop : -1.21 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 42 TYR 0.015 0.001 TYR D 118 PHE 0.009 0.001 PHE B 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.20 (13377) covalent geometry : angle 0.59998 / 0.39 (19463) hydrogen bonds : bond 0.07096 / 7.99 ( 764) hydrogen bonds : angle 3.08627 / 3.98 ( 1880) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4116.71 seconds wall clock time: 70 minutes 42.81 seconds (4242.81 seconds total)