Starting phenix.real_space_refine on Fri Sep 11 22:56:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y46_72472/09_2026/9y46_72472.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y46_72472/09_2026/9y46_72472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y46_72472/09_2026/9y46_72472.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y46_72472/09_2026/9y46_72472.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y46_72472/09_2026/9y46_72472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y46_72472/09_2026/9y46_72472.map" } resolution = 2.59 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= 0.001 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 290 5.49 5 S 12 5.16 5 C 6654 2.51 5 N 2267 2.21 5 O 2810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.00s 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: 12033 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: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} 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: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 683 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Time building chain proxies: 2.34, per 1000 atoms: 0.19 Number of scatterers: 12033 At special positions: 0 Unit cell: (113.75, 119.21, 118.3, 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 12 16.00 P 290 15.00 O 2810 8.00 N 2267 7.00 C 6654 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: 0.84 Conformation dependent library (CDL) restraints added in 327.9 milliseconds 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 71.2% alpha, 3.1% beta 144 base pairs and 270 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.551A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.576A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.737A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.522A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.618A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.523A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.538A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.551A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.584A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.781A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.572A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.508A 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 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.654A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.588A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.543A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.522A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.547A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.575A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 removed outlier: 3.512A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.666A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.740A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.908A 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 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.224A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.768A 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: 7.040A 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: 7.229A 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 78 376 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 270 stacking parallelities Total time for adding SS restraints: 2.30 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: 1946 1.33 - 1.45: 4386 1.45 - 1.57: 5905 1.57 - 1.69: 578 1.69 - 1.81: 22 Bond restraints: 12837 Sorted by residual: bond pdb=" C3' DA I -30 " pdb=" C2' DA I -30 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.50e+00 bond pdb=" C3' DC J 19 " pdb=" C2' DC J 19 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.92e+00 bond pdb=" C3' DC I -40 " pdb=" C2' DC I -40 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.72e+00 bond pdb=" C3' DG J -30 " pdb=" C2' DG J -30 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.55e+00 bond pdb=" C3' DG I 23 " pdb=" C2' DG I 23 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.33e+00 ... (remaining 12832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 16876 1.42 - 2.84: 1606 2.84 - 4.26: 79 4.26 - 5.67: 11 5.67 - 7.09: 2 Bond angle restraints: 18574 Sorted by residual: angle pdb=" N3 DT I -23 " pdb=" C4 DT I -23 " pdb=" O4 DT I -23 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT I 69 " pdb=" C4 DT I 69 " pdb=" O4 DT I 69 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT I -24 " pdb=" C4 DT I -24 " pdb=" O4 DT I -24 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT J 38 " pdb=" C4 DT J 38 " pdb=" O4 DT J 38 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT I -61 " pdb=" C4 DT I -61 " pdb=" O4 DT I -61 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 18569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.06: 5518 35.06 - 70.13: 1457 70.13 - 105.19: 3 105.19 - 140.26: 0 140.26 - 175.32: 1 Dihedral angle restraints: 6979 sinusoidal: 4758 harmonic: 2221 Sorted by residual: dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 44.68 175.32 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ASP A 77 " pdb=" CB ASP A 77 " pdb=" CG ASP A 77 " pdb=" OD1 ASP A 77 " ideal model delta sinusoidal sigma weight residual -30.00 -89.15 59.15 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 163.44 16.56 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 6976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1191 0.032 - 0.065: 626 0.065 - 0.097: 225 0.097 - 0.130: 62 0.130 - 0.162: 8 Chirality restraints: 2112 Sorted by residual: chirality pdb=" C3' DT I -59 " pdb=" C4' DT I -59 " pdb=" O3' DT I -59 " pdb=" C2' DT I -59 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" C4' DG I -35 " pdb=" C5' DG I -35 " pdb=" O4' DG I -35 " pdb=" C3' DG I -35 " both_signs ideal model delta sigma weight residual False -2.53 -2.39 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE C 78 " pdb=" N ILE C 78 " pdb=" C ILE C 78 " pdb=" CB ILE C 78 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 2109 not shown) Planarity restraints: 1345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " -0.026 2.00e-02 2.50e+03 1.15e-02 3.64e+00 pdb=" N9 DA I 47 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " -0.025 2.00e-02 2.50e+03 1.05e-02 3.33e+00 pdb=" N9 DG I -35 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I -35 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I -35 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I -35 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 17 " 0.023 2.00e-02 2.50e+03 1.05e-02 3.00e+00 pdb=" N9 DA I 17 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 17 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 17 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 17 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 17 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 17 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 17 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 17 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 17 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 17 " -0.002 2.00e-02 2.50e+03 ... (remaining 1342 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 5231 3.01 - 3.48: 9641 3.48 - 3.96: 22748 3.96 - 4.43: 26042 4.43 - 4.90: 34044 Nonbonded interactions: 97706 Sorted by model distance: nonbonded pdb=" N GLU A 59 " pdb=" OE1 GLU A 59 " model vdw 2.539 3.120 nonbonded pdb=" N GLU E 59 " pdb=" OE1 GLU E 59 " model vdw 2.567 3.120 nonbonded pdb=" N1 DG I -36 " pdb=" C4 DG I -36 " model vdw 2.591 2.672 nonbonded pdb=" N1 DG J -55 " pdb=" C4 DG J -55 " model vdw 2.591 2.672 nonbonded pdb=" N1 DG I -5 " pdb=" C4 DG I -5 " model vdw 2.593 2.672 ... (remaining 97701 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' selection = (chain 'F' and resid 21 through 101) } 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: 5.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 12.070 Find NCS groups from input model: 0.150 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:8.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 0.037 12837 Z= 0.572 Angle : 0.798 7.094 18574 Z= 0.711 Chirality : 0.044 0.162 2112 Planarity : 0.005 0.042 1345 Dihedral : 27.646 175.319 5547 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.25 % Allowed : 16.30 % Favored : 82.45 % 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: -0.97 (0.25), residues: 751 helix: -0.16 (0.19), residues: 524 sheet: None (None), residues: 0 loop : -1.58 (0.33), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 42 TYR 0.014 0.002 TYR G 57 PHE 0.019 0.002 PHE G 25 HIS 0.009 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.57 (12837) covalent geometry : angle 0.79849 / 0.71 (18574) hydrogen bonds : bond 0.22803 / 15.04 ( 744) hydrogen bonds : angle 4.35737 / 3.04 ( 1840) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.251 Fit side-chains REVERT: A 133 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8030 (mt-10) REVERT: B 77 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8348 (mtpt) REVERT: C 13 LYS cc_start: 0.6800 (OUTLIER) cc_final: 0.6538 (tmtm) REVERT: C 41 GLU cc_start: 0.8475 (tt0) cc_final: 0.7686 (mp0) REVERT: D 43 LYS cc_start: 0.8647 (mttt) cc_final: 0.8424 (mttp) REVERT: D 47 GLN cc_start: 0.8522 (mt0) cc_final: 0.8252 (mt0) REVERT: D 62 MET cc_start: 0.9245 (mmm) cc_final: 0.9015 (mmm) REVERT: D 82 HIS cc_start: 0.8258 (m170) cc_final: 0.7703 (t-90) REVERT: D 108 LYS cc_start: 0.8754 (mttm) cc_final: 0.8553 (mtpt) REVERT: F 52 GLU cc_start: 0.8503 (tp30) cc_final: 0.8217 (tp30) REVERT: F 84 MET cc_start: 0.8778 (tpt) cc_final: 0.8575 (mmt) REVERT: G 41 GLU cc_start: 0.8456 (tt0) cc_final: 0.7653 (mp0) REVERT: H 47 GLN cc_start: 0.8541 (mt0) cc_final: 0.8285 (mt0) REVERT: H 82 HIS cc_start: 0.8194 (m170) cc_final: 0.7661 (t-90) REVERT: H 108 LYS cc_start: 0.8717 (mttm) cc_final: 0.8506 (mttp) REVERT: H 116 LYS cc_start: 0.9053 (ttmt) cc_final: 0.8840 (ttpp) outliers start: 8 outliers final: 2 residues processed: 143 average time/residue: 0.9751 time to fit residues: 146.0472 Evaluate side-chains 125 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.133477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.113362 restraints weight = 11593.483| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 0.81 r_work: 0.3147 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12837 Z= 0.176 Angle : 0.682 6.621 18574 Z= 0.402 Chirality : 0.051 0.267 2112 Planarity : 0.005 0.037 1345 Dihedral : 29.857 173.130 4033 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.25 % Allowed : 15.05 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.51 (0.30), residues: 751 helix: 2.04 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.58 (0.33), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 42 TYR 0.010 0.002 TYR H 83 PHE 0.011 0.001 PHE G 25 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.18 (12837) covalent geometry : angle 0.68219 / 0.40 (18574) hydrogen bonds : bond 0.08287 / 5.56 ( 744) hydrogen bonds : angle 2.89876 / 2.09 ( 1840) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.316 Fit side-chains REVERT: A 133 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7955 (mt-10) REVERT: C 41 GLU cc_start: 0.8228 (tt0) cc_final: 0.7629 (mp0) REVERT: C 64 GLU cc_start: 0.8289 (tp30) cc_final: 0.8083 (tt0) REVERT: D 47 GLN cc_start: 0.8434 (mt0) cc_final: 0.8194 (mt0) REVERT: D 62 MET cc_start: 0.9109 (mmm) cc_final: 0.8854 (mmm) REVERT: D 71 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: G 13 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6246 (tmtm) REVERT: G 41 GLU cc_start: 0.8164 (tt0) cc_final: 0.7614 (mp0) REVERT: G 64 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: H 47 GLN cc_start: 0.8419 (mt0) cc_final: 0.8166 (mt0) REVERT: H 71 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: H 116 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8808 (ttpp) outliers start: 8 outliers final: 1 residues processed: 127 average time/residue: 0.9748 time to fit residues: 130.1411 Evaluate side-chains 123 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 62 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.132303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112224 restraints weight = 11692.703| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 0.82 r_work: 0.3128 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12837 Z= 0.172 Angle : 0.657 5.720 18574 Z= 0.388 Chirality : 0.051 0.256 2112 Planarity : 0.004 0.033 1345 Dihedral : 29.874 172.247 4023 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.72 % Allowed : 15.36 % Favored : 82.92 % 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 (0.30), residues: 751 helix: 2.50 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.57 (0.33), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.010 0.002 TYR A 54 PHE 0.015 0.002 PHE G 25 HIS 0.008 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.17 (12837) covalent geometry : angle 0.65684 / 0.39 (18574) hydrogen bonds : bond 0.08118 / 5.44 ( 744) hydrogen bonds : angle 2.80068 / 2.03 ( 1840) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.348 Fit side-chains REVERT: A 133 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7891 (mt-10) REVERT: C 41 GLU cc_start: 0.8200 (tt0) cc_final: 0.7629 (mp0) REVERT: D 47 GLN cc_start: 0.8422 (mt0) cc_final: 0.8177 (mt0) REVERT: D 62 MET cc_start: 0.9106 (mmm) cc_final: 0.8902 (mmm) REVERT: D 71 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7737 (mt-10) REVERT: F 19 ARG cc_start: 0.1312 (OUTLIER) cc_final: 0.0942 (mmp-170) REVERT: G 13 LYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6247 (tmtm) REVERT: G 41 GLU cc_start: 0.8164 (tt0) cc_final: 0.7622 (mp0) REVERT: H 47 GLN cc_start: 0.8438 (mt0) cc_final: 0.8170 (mt0) REVERT: H 71 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7774 (mt-10) outliers start: 11 outliers final: 3 residues processed: 126 average time/residue: 1.0080 time to fit residues: 133.3458 Evaluate side-chains 120 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.130754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.110642 restraints weight = 11559.751| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 0.81 r_work: 0.3104 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12837 Z= 0.189 Angle : 0.708 6.040 18574 Z= 0.409 Chirality : 0.054 0.249 2112 Planarity : 0.005 0.042 1345 Dihedral : 29.918 172.784 4023 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.19 % Allowed : 13.17 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.89 (0.30), residues: 751 helix: 2.40 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.64 (0.34), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 31 TYR 0.014 0.002 TYR A 54 PHE 0.012 0.002 PHE G 25 HIS 0.009 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.19 (12837) covalent geometry : angle 0.70776 / 0.41 (18574) hydrogen bonds : bond 0.08758 / 5.86 ( 744) hydrogen bonds : angle 2.90964 / 2.12 ( 1840) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.329 Fit side-chains REVERT: A 133 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7972 (mt-10) REVERT: C 13 LYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6240 (tmtm) REVERT: C 20 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8055 (ptp90) REVERT: C 41 GLU cc_start: 0.8231 (tt0) cc_final: 0.7652 (mp0) REVERT: D 47 GLN cc_start: 0.8436 (mt0) cc_final: 0.8178 (mt0) REVERT: D 62 MET cc_start: 0.9126 (mmm) cc_final: 0.8814 (mmm) REVERT: D 71 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: F 19 ARG cc_start: 0.1656 (OUTLIER) cc_final: 0.1153 (mmp-170) REVERT: G 13 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6449 (tmtm) REVERT: G 41 GLU cc_start: 0.8244 (tt0) cc_final: 0.7724 (mp0) REVERT: H 47 GLN cc_start: 0.8432 (mt0) cc_final: 0.8172 (mt0) REVERT: H 71 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7718 (mt-10) outliers start: 14 outliers final: 6 residues processed: 122 average time/residue: 1.0093 time to fit residues: 129.1931 Evaluate side-chains 122 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.127801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107502 restraints weight = 11557.096| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 0.82 r_work: 0.3056 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12837 Z= 0.263 Angle : 0.851 6.653 18574 Z= 0.477 Chirality : 0.064 0.240 2112 Planarity : 0.006 0.060 1345 Dihedral : 29.983 172.856 4023 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.82 % Allowed : 12.23 % Favored : 84.95 % 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: 751 helix: 1.97 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.64 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 23 TYR 0.020 0.003 TYR A 54 PHE 0.013 0.003 PHE H 70 HIS 0.013 0.003 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.26 (12837) covalent geometry : angle 0.85085 / 0.48 (18574) hydrogen bonds : bond 0.11011 / 7.37 ( 744) hydrogen bonds : angle 3.15284 / 2.29 ( 1840) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.216 Fit side-chains REVERT: C 13 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6362 (tmtm) REVERT: C 41 GLU cc_start: 0.8376 (tt0) cc_final: 0.7774 (mp0) REVERT: C 64 GLU cc_start: 0.8493 (tp30) cc_final: 0.8247 (tp30) REVERT: D 47 GLN cc_start: 0.8456 (mt0) cc_final: 0.8204 (mt0) REVERT: D 62 MET cc_start: 0.9168 (mmm) cc_final: 0.8893 (mmm) REVERT: D 71 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: F 19 ARG cc_start: 0.1664 (OUTLIER) cc_final: 0.1202 (mmp-170) REVERT: G 13 LYS cc_start: 0.6951 (OUTLIER) cc_final: 0.6505 (tmtm) REVERT: G 41 GLU cc_start: 0.8319 (tt0) cc_final: 0.7750 (mp0) REVERT: G 64 GLU cc_start: 0.8497 (tp30) cc_final: 0.8245 (tp30) REVERT: H 47 GLN cc_start: 0.8442 (mt0) cc_final: 0.8190 (mt0) REVERT: H 71 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7816 (mt-10) outliers start: 18 outliers final: 10 residues processed: 130 average time/residue: 0.9816 time to fit residues: 133.9910 Evaluate side-chains 127 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.128167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108638 restraints weight = 11805.367| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 0.73 r_work: 0.3077 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12837 Z= 0.250 Angle : 0.832 6.494 18574 Z= 0.467 Chirality : 0.063 0.242 2112 Planarity : 0.006 0.052 1345 Dihedral : 29.990 172.609 4023 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.29 % Allowed : 12.07 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.28 (0.29), residues: 751 helix: 1.90 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.85 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 39 TYR 0.016 0.002 TYR A 54 PHE 0.011 0.003 PHE F 61 HIS 0.011 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.25 (12837) covalent geometry : angle 0.83158 / 0.47 (18574) hydrogen bonds : bond 0.10561 / 7.07 ( 744) hydrogen bonds : angle 3.15605 / 2.30 ( 1840) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.336 Fit side-chains REVERT: A 115 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8355 (mtpt) REVERT: B 91 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8224 (ttpm) REVERT: C 13 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6337 (tmtm) REVERT: C 41 GLU cc_start: 0.8305 (tt0) cc_final: 0.7776 (mp0) REVERT: C 64 GLU cc_start: 0.8470 (tp30) cc_final: 0.8235 (tp30) REVERT: D 47 GLN cc_start: 0.8455 (mt0) cc_final: 0.8210 (mt0) REVERT: D 62 MET cc_start: 0.9131 (mmm) cc_final: 0.8865 (mmm) REVERT: D 71 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7736 (mt-10) REVERT: E 115 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8339 (mtpt) REVERT: F 19 ARG cc_start: 0.1804 (OUTLIER) cc_final: 0.1301 (mmp-170) REVERT: G 13 LYS cc_start: 0.6942 (OUTLIER) cc_final: 0.6379 (tmtm) REVERT: G 41 GLU cc_start: 0.8271 (tt0) cc_final: 0.7768 (mp0) REVERT: G 64 GLU cc_start: 0.8477 (tp30) cc_final: 0.8225 (tp30) REVERT: H 47 GLN cc_start: 0.8439 (mt0) cc_final: 0.8173 (mt0) REVERT: H 71 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7775 (mt-10) outliers start: 21 outliers final: 9 residues processed: 128 average time/residue: 1.0436 time to fit residues: 140.1083 Evaluate side-chains 129 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 chunk 58 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.132049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112759 restraints weight = 11847.331| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 0.72 r_work: 0.3144 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12837 Z= 0.177 Angle : 0.701 6.006 18574 Z= 0.405 Chirality : 0.053 0.254 2112 Planarity : 0.005 0.040 1345 Dihedral : 29.953 174.504 4023 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.51 % Allowed : 12.85 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.69 (0.30), residues: 751 helix: 2.23 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.79 (0.34), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 131 TYR 0.011 0.002 TYR H 121 PHE 0.008 0.002 PHE F 61 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.18 (12837) covalent geometry : angle 0.70150 / 0.41 (18574) hydrogen bonds : bond 0.07988 / 5.37 ( 744) hydrogen bonds : angle 3.05990 / 2.24 ( 1840) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.337 Fit side-chains REVERT: B 91 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8182 (ttpm) REVERT: C 13 LYS cc_start: 0.6817 (OUTLIER) cc_final: 0.6229 (tmtm) REVERT: C 20 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7691 (ptp90) REVERT: C 35 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7490 (mtp-110) REVERT: C 41 GLU cc_start: 0.8251 (tt0) cc_final: 0.7717 (mp0) REVERT: D 47 GLN cc_start: 0.8421 (mt0) cc_final: 0.8175 (mt0) REVERT: D 62 MET cc_start: 0.9039 (mmm) cc_final: 0.8798 (mmm) REVERT: D 71 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: E 133 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7813 (mt-10) REVERT: F 19 ARG cc_start: 0.1686 (OUTLIER) cc_final: 0.1217 (mmp-170) REVERT: G 13 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6337 (tmtm) REVERT: G 41 GLU cc_start: 0.8192 (tt0) cc_final: 0.7710 (mp0) REVERT: H 47 GLN cc_start: 0.8395 (mt0) cc_final: 0.8143 (mt0) REVERT: H 71 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7697 (mt-10) outliers start: 16 outliers final: 5 residues processed: 125 average time/residue: 1.0325 time to fit residues: 135.5254 Evaluate side-chains 128 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 64 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 0.0000 chunk 25 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 0.0870 chunk 90 optimal weight: 10.0000 overall best weight: 0.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113644 restraints weight = 11764.730| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 0.71 r_work: 0.3158 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12837 Z= 0.165 Angle : 0.657 5.840 18574 Z= 0.386 Chirality : 0.051 0.259 2112 Planarity : 0.004 0.033 1345 Dihedral : 29.923 173.322 4023 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.19 % Allowed : 13.01 % Favored : 84.80 % 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: 2.09 (0.30), residues: 751 helix: 2.57 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.64 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.007 0.001 TYR A 54 PHE 0.010 0.001 PHE F 61 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.17 (12837) covalent geometry : angle 0.65715 / 0.39 (18574) hydrogen bonds : bond 0.07616 / 5.11 ( 744) hydrogen bonds : angle 2.81472 / 2.06 ( 1840) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.331 Fit side-chains REVERT: C 13 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6259 (tmtm) REVERT: C 20 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7672 (ptp90) REVERT: C 41 GLU cc_start: 0.8240 (tt0) cc_final: 0.7709 (mp0) REVERT: D 47 GLN cc_start: 0.8406 (mt0) cc_final: 0.8153 (mt0) REVERT: D 71 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: E 133 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7816 (mt-10) REVERT: F 19 ARG cc_start: 0.1732 (OUTLIER) cc_final: 0.1247 (mmp-170) REVERT: G 13 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6282 (tmtm) REVERT: G 41 GLU cc_start: 0.8183 (tt0) cc_final: 0.7680 (mp0) REVERT: H 47 GLN cc_start: 0.8398 (mt0) cc_final: 0.8147 (mt0) REVERT: H 71 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7723 (mt-10) outliers start: 14 outliers final: 6 residues processed: 120 average time/residue: 1.0378 time to fit residues: 130.4959 Evaluate side-chains 123 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.130954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.111683 restraints weight = 11704.522| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 0.72 r_work: 0.3126 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12837 Z= 0.184 Angle : 0.697 5.890 18574 Z= 0.404 Chirality : 0.054 0.250 2112 Planarity : 0.005 0.037 1345 Dihedral : 29.970 173.598 4023 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.66 % Allowed : 12.85 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.89 (0.30), residues: 751 helix: 2.41 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -1.76 (0.35), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 39 TYR 0.011 0.002 TYR A 54 PHE 0.011 0.002 PHE F 61 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.18 (12837) covalent geometry : angle 0.69689 / 0.40 (18574) hydrogen bonds : bond 0.08461 / 5.67 ( 744) hydrogen bonds : angle 2.88163 / 2.11 ( 1840) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.384 Fit side-chains REVERT: B 91 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8198 (ttpm) REVERT: C 13 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6303 (tmtm) REVERT: C 20 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7712 (ptp90) REVERT: C 41 GLU cc_start: 0.8255 (tt0) cc_final: 0.7758 (mp0) REVERT: D 47 GLN cc_start: 0.8411 (mt0) cc_final: 0.8157 (mt0) REVERT: D 71 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: D 85 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8379 (mmtm) REVERT: E 133 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7843 (mt-10) REVERT: F 19 ARG cc_start: 0.1868 (OUTLIER) cc_final: 0.1347 (mmp-170) REVERT: G 13 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6263 (tmtm) REVERT: G 41 GLU cc_start: 0.8206 (tt0) cc_final: 0.7712 (mp0) REVERT: H 47 GLN cc_start: 0.8409 (mt0) cc_final: 0.8154 (mt0) REVERT: H 71 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7761 (mt-10) outliers start: 17 outliers final: 5 residues processed: 124 average time/residue: 1.0061 time to fit residues: 130.7710 Evaluate side-chains 127 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 34 optimal weight: 0.4980 chunk 85 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.109969 restraints weight = 11775.702| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 0.73 r_work: 0.3098 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12837 Z= 0.215 Angle : 0.762 6.079 18574 Z= 0.434 Chirality : 0.058 0.245 2112 Planarity : 0.005 0.045 1345 Dihedral : 30.003 173.835 4023 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.19 % Allowed : 13.32 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.63 (0.30), residues: 751 helix: 2.17 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.76 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 39 TYR 0.015 0.002 TYR A 54 PHE 0.011 0.002 PHE F 61 HIS 0.008 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.21 (12837) covalent geometry : angle 0.76190 / 0.43 (18574) hydrogen bonds : bond 0.09630 / 6.46 ( 744) hydrogen bonds : angle 3.00717 / 2.19 ( 1840) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.304 Fit side-chains REVERT: C 13 LYS cc_start: 0.6918 (OUTLIER) cc_final: 0.6260 (tmtm) REVERT: C 20 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8073 (ptp90) REVERT: C 41 GLU cc_start: 0.8278 (tt0) cc_final: 0.7792 (mp0) REVERT: C 64 GLU cc_start: 0.8464 (tp30) cc_final: 0.8219 (tp30) REVERT: D 47 GLN cc_start: 0.8449 (mt0) cc_final: 0.8195 (mt0) REVERT: D 71 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7720 (mt-10) REVERT: D 85 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8402 (mmtm) REVERT: E 133 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7847 (mt-10) REVERT: F 19 ARG cc_start: 0.1955 (OUTLIER) cc_final: 0.1368 (mmp-170) REVERT: G 13 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6348 (tmtm) REVERT: G 41 GLU cc_start: 0.8217 (tt0) cc_final: 0.7729 (mp0) REVERT: G 64 GLU cc_start: 0.8476 (tp30) cc_final: 0.8212 (tp30) REVERT: H 47 GLN cc_start: 0.8428 (mt0) cc_final: 0.8153 (mt0) REVERT: H 71 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7760 (mt-10) outliers start: 14 outliers final: 4 residues processed: 125 average time/residue: 1.0009 time to fit residues: 131.1445 Evaluate side-chains 123 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 6.9990 chunk 9 optimal weight: 0.1980 chunk 2 optimal weight: 0.0570 chunk 3 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.131456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.112178 restraints weight = 11740.234| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 0.72 r_work: 0.3134 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12837 Z= 0.164 Angle : 0.689 5.964 18574 Z= 0.401 Chirality : 0.053 0.257 2112 Planarity : 0.005 0.035 1345 Dihedral : 29.981 174.157 4023 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.57 % Allowed : 13.95 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.70 (0.30), residues: 751 helix: 2.21 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.75 (0.35), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 131 TYR 0.010 0.001 TYR D 37 PHE 0.010 0.001 PHE F 61 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.16 (12837) covalent geometry : angle 0.68899 / 0.40 (18574) hydrogen bonds : bond 0.08205 / 5.50 ( 744) hydrogen bonds : angle 3.08154 / 2.26 ( 1840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4407.39 seconds wall clock time: 75 minutes 34.71 seconds (4534.71 seconds total)