Starting phenix.real_space_refine on Fri Jul 3 04:33:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y46_72472/07_2026/9y46_72472.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y46_72472/07_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_72472/07_2026/9y46_72472.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y46_72472/07_2026/9y46_72472.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y46_72472/07_2026/9y46_72472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y46_72472/07_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): 0.01s 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: 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: 2.39, per 1000 atoms: 0.20 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 178.1 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: 1.40 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: 1.74 Time building geometry restraints manager: 1.13 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: 16966 1.42 - 2.84: 1516 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: 4.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.690 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:7.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.820 ------------------------------------------------------------------------------- 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 : 0.789 7.094 18574 Z= 0.702 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 0.78857 / 0.70 (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 : 0.325 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: 0.8347 (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: 0.7685 (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: 0.7704 (t-90) REVERT: D 86 ARG cc_start: 0.8688 (mmt90) cc_final: 0.8426 (mmt90) 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: 0.7652 (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 86 ARG cc_start: 0.8653 (mmt90) cc_final: 0.8338 (mmt90) 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: 0.8989 time to fit residues: 134.6744 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 : 0.316 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.133491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.113378 restraints weight = 11600.799| |-----------------------------------------------------------------------------| 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: 3.02 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12837 Z= 0.172 Angle : 0.673 6.569 18574 Z= 0.400 Chirality : 0.050 0.254 2112 Planarity : 0.004 0.037 1345 Dihedral : 29.914 174.015 4033 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: 1.49 (0.30), residues: 751 helix: 2.03 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.59 (0.33), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 42 TYR 0.011 0.002 TYR H 83 PHE 0.010 0.001 PHE C 25 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.17 (12837) covalent geometry : angle 0.67289 / 0.40 (18574) hydrogen bonds : bond 0.08194 / 5.50 ( 744) hydrogen bonds : angle 2.91670 / 2.11 ( 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 : 0.267 Fit side-chains REVERT: A 133 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7951 (mt-10) REVERT: C 41 GLU cc_start: 0.8215 (tt0) cc_final: 0.7619 (mp0) REVERT: C 64 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: D 47 GLN cc_start: 0.8430 (mt0) cc_final: 0.8190 (mt0) REVERT: D 62 MET cc_start: 0.9108 (mmm) cc_final: 0.8863 (mmm) REVERT: D 71 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: D 86 ARG cc_start: 0.8602 (mmt90) cc_final: 0.8397 (mmt90) REVERT: G 13 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6246 (tmtm) REVERT: G 41 GLU cc_start: 0.8157 (tt0) cc_final: 0.7632 (mp0) REVERT: G 64 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: H 47 GLN cc_start: 0.8416 (mt0) cc_final: 0.8161 (mt0) REVERT: H 71 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: H 86 ARG cc_start: 0.8556 (mmt90) cc_final: 0.8317 (mmt90) REVERT: H 116 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8804 (ttpp) outliers start: 8 outliers final: 1 residues processed: 126 average time/residue: 0.8255 time to fit residues: 109.3051 Evaluate side-chains 124 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU 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: 0.8980 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 62 optimal weight: 0.0570 chunk 27 optimal weight: 0.9980 overall best weight: 0.7700 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.133093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.113027 restraints weight = 11704.770| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 0.81 r_work: 0.3149 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1410 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= 0.164 Angle : 0.626 5.613 18574 Z= 0.376 Chirality : 0.048 0.235 2112 Planarity : 0.004 0.033 1345 Dihedral : 29.924 172.677 4023 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.04 % Allowed : 14.73 % Favored : 83.23 % 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: 2.12 (0.30), residues: 751 helix: 2.56 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.54 (0.33), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.009 0.001 TYR A 54 PHE 0.014 0.002 PHE C 25 HIS 0.007 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.16 (12837) covalent geometry : angle 0.62618 / 0.38 (18574) hydrogen bonds : bond 0.07700 / 5.16 ( 744) hydrogen bonds : angle 2.73679 / 1.99 ( 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 131 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.308 Fit side-chains REVERT: A 133 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7922 (mt-10) REVERT: C 13 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6842 (tmtm) REVERT: C 41 GLU cc_start: 0.8201 (tt0) cc_final: 0.7598 (mp0) REVERT: D 47 GLN cc_start: 0.8409 (mt0) cc_final: 0.8161 (mt0) REVERT: D 62 MET cc_start: 0.9074 (mmm) cc_final: 0.8846 (mmm) REVERT: D 71 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: F 19 ARG cc_start: 0.1303 (OUTLIER) cc_final: 0.0939 (mmp-170) REVERT: G 13 LYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6253 (tmtm) REVERT: G 41 GLU cc_start: 0.8157 (tt0) cc_final: 0.7592 (mp0) REVERT: G 64 GLU cc_start: 0.8313 (tp30) cc_final: 0.8059 (tp30) REVERT: H 47 GLN cc_start: 0.8420 (mt0) cc_final: 0.8176 (mt0) REVERT: H 71 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7777 (mt-10) outliers start: 13 outliers final: 4 residues processed: 127 average time/residue: 0.8120 time to fit residues: 108.2919 Evaluate side-chains 123 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 LYS 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 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: 2.9990 chunk 97 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 40 optimal weight: 0.0870 chunk 68 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 98 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- 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 = 0.130715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110583 restraints weight = 11556.295| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 0.81 r_work: 0.3101 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12837 Z= 0.191 Angle : 0.695 5.846 18574 Z= 0.404 Chirality : 0.054 0.227 2112 Planarity : 0.005 0.039 1345 Dihedral : 29.973 173.714 4023 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.19 % Allowed : 13.95 % Favored : 83.86 % 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: 1.96 (0.30), residues: 751 helix: 2.45 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.61 (0.33), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 42 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 0.00335 / 0.19 (12837) covalent geometry : angle 0.69485 / 0.40 (18574) hydrogen bonds : bond 0.08708 / 5.83 ( 744) hydrogen bonds : angle 2.88733 / 2.10 ( 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 127 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.222 Fit side-chains REVERT: A 133 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7886 (mt-10) REVERT: C 20 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7751 (ptp90) REVERT: C 41 GLU cc_start: 0.8234 (tt0) cc_final: 0.7656 (mp0) REVERT: D 47 GLN cc_start: 0.8428 (mt0) cc_final: 0.8187 (mt0) REVERT: D 62 MET cc_start: 0.9117 (mmm) cc_final: 0.8806 (mmm) REVERT: D 71 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7670 (mt-10) REVERT: F 19 ARG cc_start: 0.1563 (OUTLIER) cc_final: 0.1125 (mmp-170) REVERT: G 13 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6332 (tmtm) REVERT: G 41 GLU cc_start: 0.8235 (tt0) cc_final: 0.7720 (mp0) REVERT: H 47 GLN cc_start: 0.8432 (mt0) cc_final: 0.8170 (mt0) REVERT: H 71 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7715 (mt-10) outliers start: 14 outliers final: 7 residues processed: 124 average time/residue: 0.8670 time to fit residues: 112.9499 Evaluate side-chains 121 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 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=3.50 ------------------------------------------------------------------------------- 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: 0.5980 chunk 53 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.128655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108410 restraints weight = 11584.003| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 0.82 r_work: 0.3069 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12837 Z= 0.231 Angle : 0.779 6.148 18574 Z= 0.444 Chirality : 0.059 0.229 2112 Planarity : 0.006 0.053 1345 Dihedral : 30.015 174.001 4023 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.98 % Allowed : 12.85 % Favored : 84.17 % 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: 1.59 (0.30), residues: 751 helix: 2.15 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.68 (0.34), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 40 TYR 0.017 0.002 TYR A 54 PHE 0.012 0.003 PHE C 25 HIS 0.011 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.23 (12837) covalent geometry : angle 0.77890 / 0.44 (18574) hydrogen bonds : bond 0.10103 / 6.76 ( 744) hydrogen bonds : angle 3.06293 / 2.23 ( 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 137 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.331 Fit side-chains REVERT: C 13 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6291 (tmtm) REVERT: C 20 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8006 (ptp90) REVERT: C 41 GLU cc_start: 0.8324 (tt0) cc_final: 0.7753 (mp0) REVERT: D 47 GLN cc_start: 0.8460 (mt0) cc_final: 0.8211 (mt0) REVERT: D 62 MET cc_start: 0.9132 (mmm) cc_final: 0.8868 (mmm) REVERT: D 71 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: F 19 ARG cc_start: 0.1630 (OUTLIER) cc_final: 0.1191 (mmp-170) REVERT: G 13 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6415 (tmtm) REVERT: G 41 GLU cc_start: 0.8289 (tt0) cc_final: 0.7729 (mp0) REVERT: H 47 GLN cc_start: 0.8451 (mt0) cc_final: 0.8198 (mt0) REVERT: H 71 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7750 (mt-10) outliers start: 19 outliers final: 8 residues processed: 131 average time/residue: 1.0196 time to fit residues: 139.9479 Evaluate side-chains 125 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 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 77 ASP 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: 10.0000 chunk 92 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.128179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.108712 restraints weight = 11839.481| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 0.73 r_work: 0.3079 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1646 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= 0.249 Angle : 0.821 6.445 18574 Z= 0.464 Chirality : 0.062 0.247 2112 Planarity : 0.006 0.057 1345 Dihedral : 30.091 174.332 4023 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.98 % Allowed : 12.54 % 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: 1.32 (0.29), residues: 751 helix: 1.93 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.81 (0.35), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 77 TYR 0.017 0.002 TYR A 54 PHE 0.012 0.003 PHE D 70 HIS 0.011 0.002 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.25 (12837) covalent geometry : angle 0.82109 / 0.46 (18574) hydrogen bonds : bond 0.10488 / 7.02 ( 744) hydrogen bonds : angle 3.11946 / 2.27 ( 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: 19 poor density : 117 time to evaluate : 0.204 Fit side-chains REVERT: B 91 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8216 (ttpm) REVERT: C 13 LYS cc_start: 0.6873 (OUTLIER) cc_final: 0.6262 (tmtm) REVERT: C 20 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8122 (ptp90) REVERT: C 41 GLU cc_start: 0.8301 (tt0) cc_final: 0.7784 (mp0) REVERT: C 64 GLU cc_start: 0.8471 (tp30) cc_final: 0.8210 (tp30) REVERT: D 47 GLN cc_start: 0.8471 (mt0) cc_final: 0.8209 (mt0) REVERT: D 62 MET cc_start: 0.9125 (mmm) cc_final: 0.8858 (mmm) REVERT: D 71 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7677 (mt-10) REVERT: E 115 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8320 (mtpt) REVERT: E 133 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7869 (mt-10) REVERT: F 19 ARG cc_start: 0.1805 (OUTLIER) cc_final: 0.1209 (mmp-170) REVERT: G 13 LYS cc_start: 0.6946 (OUTLIER) cc_final: 0.6387 (tmtm) REVERT: G 41 GLU cc_start: 0.8270 (tt0) cc_final: 0.7761 (mp0) REVERT: G 64 GLU cc_start: 0.8435 (tp30) cc_final: 0.8181 (tp30) REVERT: H 47 GLN cc_start: 0.8453 (mt0) cc_final: 0.8189 (mt0) REVERT: H 71 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7722 (mt-10) outliers start: 19 outliers final: 8 residues processed: 128 average time/residue: 0.8688 time to fit residues: 116.8076 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 : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU 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 19 SER 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: 0.7980 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 41 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.130641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111272 restraints weight = 11819.604| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 0.73 r_work: 0.3120 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1684 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= 0.173 Angle : 0.713 6.011 18574 Z= 0.415 Chirality : 0.055 0.241 2112 Planarity : 0.005 0.037 1345 Dihedral : 30.072 174.925 4023 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.19 % Allowed : 14.11 % 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: 1.55 (0.30), residues: 751 helix: 2.10 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.79 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 35 TYR 0.010 0.001 TYR A 54 PHE 0.010 0.002 PHE F 61 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.17 (12837) covalent geometry : angle 0.71301 / 0.41 (18574) hydrogen bonds : bond 0.08495 / 5.70 ( 744) hydrogen bonds : angle 3.18712 / 2.33 ( 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 128 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.281 Fit side-chains REVERT: B 91 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8183 (ttpm) REVERT: C 13 LYS cc_start: 0.6871 (OUTLIER) cc_final: 0.6233 (tmtm) REVERT: C 35 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7527 (mtp-110) REVERT: C 41 GLU cc_start: 0.8269 (tt0) cc_final: 0.7720 (mp0) REVERT: D 47 GLN cc_start: 0.8440 (mt0) cc_final: 0.8181 (mt0) REVERT: D 62 MET cc_start: 0.9044 (mmm) cc_final: 0.8800 (mmm) REVERT: D 71 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: E 133 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7846 (mt-10) REVERT: F 19 ARG cc_start: 0.1762 (OUTLIER) cc_final: 0.1208 (mmp-170) REVERT: G 13 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6258 (tmtm) REVERT: G 41 GLU cc_start: 0.8213 (tt0) cc_final: 0.7715 (mp0) REVERT: H 47 GLN cc_start: 0.8417 (mt0) cc_final: 0.8153 (mt0) REVERT: H 71 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7668 (mt-10) outliers start: 14 outliers final: 4 residues processed: 120 average time/residue: 0.8880 time to fit residues: 111.6798 Evaluate side-chains 125 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 35 ARG Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 77 ASP 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 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: 0.0870 chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.0060 chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 0.0270 chunk 90 optimal weight: 10.0000 overall best weight: 0.3832 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.131856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112622 restraints weight = 11794.534| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 0.72 r_work: 0.3140 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12837 Z= 0.173 Angle : 0.684 6.040 18574 Z= 0.403 Chirality : 0.052 0.237 2112 Planarity : 0.004 0.034 1345 Dihedral : 30.045 175.474 4023 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.51 % Allowed : 13.48 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.90 (0.30), residues: 751 helix: 2.37 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.71 (0.35), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 134 TYR 0.008 0.001 TYR D 37 PHE 0.009 0.001 PHE F 61 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.17 (12837) covalent geometry : angle 0.68430 / 0.40 (18574) hydrogen bonds : bond 0.08167 / 5.49 ( 744) hydrogen bonds : angle 2.88510 / 2.11 ( 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 131 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.265 Fit side-chains REVERT: C 13 LYS cc_start: 0.6855 (OUTLIER) cc_final: 0.6218 (tmtm) REVERT: C 35 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7543 (mtp-110) REVERT: C 41 GLU cc_start: 0.8263 (tt0) cc_final: 0.7715 (mp0) REVERT: D 47 GLN cc_start: 0.8419 (mt0) cc_final: 0.8158 (mt0) REVERT: D 62 MET cc_start: 0.9032 (mmm) cc_final: 0.8798 (mmm) REVERT: D 71 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: E 73 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8494 (tt0) REVERT: E 133 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7846 (mt-10) REVERT: F 19 ARG cc_start: 0.1859 (OUTLIER) cc_final: 0.1299 (mmp-170) REVERT: F 91 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8189 (ttpm) REVERT: G 13 LYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6310 (tmtm) REVERT: G 41 GLU cc_start: 0.8193 (tt0) cc_final: 0.7692 (mp0) REVERT: H 47 GLN cc_start: 0.8386 (mt0) cc_final: 0.8128 (mt0) REVERT: H 71 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7665 (mt-10) outliers start: 16 outliers final: 4 residues processed: 121 average time/residue: 0.8772 time to fit residues: 111.3726 Evaluate side-chains 126 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 35 ARG Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 73 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 F residue 91 LYS 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: 0.7980 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.131499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112374 restraints weight = 11748.254| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 0.72 r_work: 0.3137 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12837 Z= 0.174 Angle : 0.670 5.739 18574 Z= 0.395 Chirality : 0.052 0.237 2112 Planarity : 0.004 0.035 1345 Dihedral : 30.045 174.373 4023 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.19 % Allowed : 14.11 % 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: 1.97 (0.30), residues: 751 helix: 2.44 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.70 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 39 TYR 0.010 0.001 TYR A 54 PHE 0.011 0.002 PHE F 61 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.17 (12837) covalent geometry : angle 0.67034 / 0.39 (18574) hydrogen bonds : bond 0.08134 / 5.45 ( 744) hydrogen bonds : angle 2.84877 / 2.08 ( 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 129 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.193 Fit side-chains REVERT: C 13 LYS cc_start: 0.6897 (OUTLIER) cc_final: 0.6269 (tmtm) REVERT: C 35 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7574 (mtp-110) REVERT: C 41 GLU cc_start: 0.8258 (tt0) cc_final: 0.7751 (mp0) REVERT: C 64 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: D 47 GLN cc_start: 0.8416 (mt0) cc_final: 0.8158 (mt0) REVERT: D 71 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: E 133 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7850 (mt-10) REVERT: F 19 ARG cc_start: 0.1975 (OUTLIER) cc_final: 0.1388 (mmp-170) REVERT: F 91 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8179 (ttpm) REVERT: G 13 LYS cc_start: 0.6917 (OUTLIER) cc_final: 0.6246 (tmtm) REVERT: G 41 GLU cc_start: 0.8190 (tt0) cc_final: 0.7716 (mp0) REVERT: H 47 GLN cc_start: 0.8404 (mt0) cc_final: 0.8144 (mt0) REVERT: H 71 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7650 (mt-10) outliers start: 14 outliers final: 6 residues processed: 122 average time/residue: 0.8708 time to fit residues: 111.4872 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 : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU 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 35 ARG Chi-restraints excluded: chain C residue 64 GLU 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 F residue 91 LYS 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: 1.9990 chunk 70 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 77 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 34 optimal weight: 0.3980 chunk 85 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.131579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112449 restraints weight = 11834.599| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 0.72 r_work: 0.3140 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1792 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 : 0.669 5.638 18574 Z= 0.394 Chirality : 0.052 0.234 2112 Planarity : 0.004 0.035 1345 Dihedral : 30.047 174.460 4023 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.19 % Allowed : 13.95 % Favored : 83.86 % 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 (0.30), residues: 751 helix: 2.44 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.69 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 86 TYR 0.010 0.001 TYR A 54 PHE 0.011 0.002 PHE F 61 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.17 (12837) covalent geometry : angle 0.66901 / 0.39 (18574) hydrogen bonds : bond 0.08102 / 5.43 ( 744) hydrogen bonds : angle 2.84181 / 2.08 ( 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 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: B 91 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8176 (ttpm) REVERT: C 13 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6288 (tmtm) REVERT: C 35 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7575 (mtp-110) REVERT: C 41 GLU cc_start: 0.8260 (tt0) cc_final: 0.7734 (mp0) REVERT: C 64 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7892 (tt0) REVERT: D 47 GLN cc_start: 0.8420 (mt0) cc_final: 0.8160 (mt0) REVERT: D 71 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7620 (mt-10) REVERT: E 133 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7854 (mt-10) REVERT: F 19 ARG cc_start: 0.1971 (OUTLIER) cc_final: 0.1384 (mmp-170) REVERT: F 91 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8182 (ttpm) REVERT: G 13 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6242 (tmtm) REVERT: G 41 GLU cc_start: 0.8200 (tt0) cc_final: 0.7706 (mp0) REVERT: H 47 GLN cc_start: 0.8405 (mt0) cc_final: 0.8143 (mt0) REVERT: H 71 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7657 (mt-10) outliers start: 14 outliers final: 4 residues processed: 119 average time/residue: 1.0210 time to fit residues: 127.3637 Evaluate side-chains 125 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU 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 35 ARG Chi-restraints excluded: chain C residue 64 GLU 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 F residue 91 LYS Chi-restraints excluded: chain G residue 13 LYS 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: 4.9990 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.131390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.112251 restraints weight = 11731.004| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 0.72 r_work: 0.3137 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12837 Z= 0.179 Angle : 0.678 5.566 18574 Z= 0.396 Chirality : 0.052 0.230 2112 Planarity : 0.004 0.033 1345 Dihedral : 30.054 174.593 4023 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.04 % Allowed : 13.95 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.93 (0.30), residues: 751 helix: 2.40 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.69 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 39 TYR 0.010 0.001 TYR A 54 PHE 0.010 0.002 PHE F 61 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.18 (12837) covalent geometry : angle 0.67766 / 0.40 (18574) hydrogen bonds : bond 0.08201 / 5.50 ( 744) hydrogen bonds : angle 2.82476 / 2.07 ( 1840) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3930.83 seconds wall clock time: 67 minutes 24.83 seconds (4044.83 seconds total)