Starting phenix.real_space_refine on Fri Jul 3 03:50:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y47_72473/07_2026/9y47_72473.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y47_72473/07_2026/9y47_72473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y47_72473/07_2026/9y47_72473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y47_72473/07_2026/9y47_72473.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y47_72473/07_2026/9y47_72473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y47_72473/07_2026/9y47_72473.map" } resolution = 2.74 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= 0.002 sd= 0.031 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 6598 2.51 5 N 2245 2.21 5 O 2798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s 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: 11943 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: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} 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: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} 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: 2.27, per 1000 atoms: 0.19 Number of scatterers: 11943 At special positions: 0 Unit cell: (119.21, 102.83, 120.12, 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 2798 8.00 N 2245 7.00 C 6598 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: 0.94 Conformation dependent library (CDL) restraints added in 169.0 milliseconds 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 72.7% alpha, 2.9% beta 144 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.610A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.928A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.750A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 77 removed outlier: 4.073A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.537A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.814A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.690A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.582A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 removed outlier: 3.526A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.684A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.530A 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 104 through 124 removed outlier: 3.599A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (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: 3.956A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.547A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.101A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.770A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.772A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.624A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.525A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (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: 3.857A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.833A 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: 6.857A 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: 7.306A 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 100 through 102 removed outlier: 6.694A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.970A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.195A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 386 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 1.30 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: 2014 1.33 - 1.45: 4312 1.45 - 1.57: 5820 1.57 - 1.69: 578 1.69 - 1.80: 22 Bond restraints: 12746 Sorted by residual: bond pdb=" C3' DG I 20 " pdb=" C2' DG I 20 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.30e+01 bond pdb=" C3' DA J 65 " pdb=" C2' DA J 65 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.27e+01 bond pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DC I -40 " pdb=" C2' DC I -40 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DC J -23 " pdb=" C2' DC J -23 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.58e+00 ... (remaining 12741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 16162 1.15 - 2.30: 1869 2.30 - 3.45: 403 3.45 - 4.60: 15 4.60 - 5.75: 4 Bond angle restraints: 18453 Sorted by residual: angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT J -43 " pdb=" C4 DT J -43 " pdb=" O4 DT J -43 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT J 31 " pdb=" C4 DT J 31 " pdb=" O4 DT J 31 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT I -50 " pdb=" C4 DT I -50 " pdb=" O4 DT I -50 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT I -61 " pdb=" C4 DT I -61 " pdb=" O4 DT I -61 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 18448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 5496 34.78 - 69.55: 1418 69.55 - 104.33: 5 104.33 - 139.11: 0 139.11 - 173.88: 1 Dihedral angle restraints: 6920 sinusoidal: 4729 harmonic: 2191 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 46.12 173.88 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 -89.73 59.73 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CG ARG E 52 " pdb=" CD ARG E 52 " pdb=" NE ARG E 52 " pdb=" CZ ARG E 52 " ideal model delta sinusoidal sigma weight residual 180.00 135.67 44.33 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 6917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1204 0.035 - 0.070: 653 0.070 - 0.105: 203 0.105 - 0.140: 34 0.140 - 0.175: 4 Chirality restraints: 2098 Sorted by residual: chirality pdb=" CA ASN G 73 " pdb=" N ASN G 73 " pdb=" C ASN G 73 " pdb=" CB ASN G 73 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA ASN C 73 " pdb=" N ASN C 73 " pdb=" C ASN C 73 " pdb=" CB ASN C 73 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.73e-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 -2.38 -0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 2095 not shown) Planarity restraints: 1330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 17 " -0.026 2.00e-02 2.50e+03 1.15e-02 3.61e+00 pdb=" N9 DA I 17 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DA I 17 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 17 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 17 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 17 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 17 " -0.007 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 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 17 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 108 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.42e+00 pdb=" N PRO C 109 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 109 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 109 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " -0.025 2.00e-02 2.50e+03 1.03e-02 3.20e+00 pdb=" N9 DG I -35 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " -0.002 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 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " 0.002 2.00e-02 2.50e+03 ... (remaining 1327 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1927 2.78 - 3.31: 9138 3.31 - 3.84: 21490 3.84 - 4.37: 26178 4.37 - 4.90: 37615 Nonbonded interactions: 96348 Sorted by model distance: nonbonded pdb=" O SER H 124 " pdb=" OG SER H 124 " model vdw 2.254 3.040 nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 59 " model vdw 2.415 3.040 nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.440 3.040 nonbonded pdb=" N ASP H 51 " pdb=" OD1 ASP H 51 " model vdw 2.450 3.120 nonbonded pdb=" N ASP D 51 " pdb=" OD1 ASP D 51 " model vdw 2.461 3.120 ... (remaining 96343 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 101) selection = (chain 'F' and resid 25 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: 0.960 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.010 Process input model: 10.550 Find NCS groups from input model: 0.090 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:7.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 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 0.036 12746 Z= 0.568 Angle : 0.769 5.751 18453 Z= 0.698 Chirality : 0.045 0.175 2098 Planarity : 0.004 0.046 1330 Dihedral : 27.271 173.884 5508 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.39 % Allowed : 20.06 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.31), residues: 741 helix: 2.79 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.76 (0.32), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 129 TYR 0.011 0.002 TYR D 121 PHE 0.010 0.002 PHE C 25 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.57 (12746) covalent geometry : angle 0.76933 / 0.70 (18453) hydrogen bonds : bond 0.10641 / 7.25 ( 756) hydrogen bonds : angle 3.14648 / 2.30 ( 1874) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.235 Fit side-chains REVERT: A 120 MET cc_start: 0.7743 (mtt) cc_final: 0.7430 (mtt) REVERT: B 78 ARG cc_start: 0.8604 (mtm110) cc_final: 0.8372 (mtm-85) REVERT: C 42 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7966 (ptp-170) REVERT: D 84 ASN cc_start: 0.8416 (m-40) cc_final: 0.8169 (m-40) REVERT: D 85 LYS cc_start: 0.8444 (mmtp) cc_final: 0.8118 (mttp) REVERT: G 13 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7011 (tmtm) REVERT: G 62 ILE cc_start: 0.8241 (mt) cc_final: 0.7913 (tt) REVERT: G 64 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: G 99 LYS cc_start: 0.8376 (mmtm) cc_final: 0.8121 (mmtm) REVERT: H 62 MET cc_start: 0.8446 (mmp) cc_final: 0.8131 (mmm) REVERT: H 85 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8162 (mptt) REVERT: H 116 LYS cc_start: 0.8689 (ttmt) cc_final: 0.8440 (ttpp) outliers start: 15 outliers final: 8 residues processed: 169 average time/residue: 0.8172 time to fit residues: 145.3554 Evaluate side-chains 175 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 91 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN C 24 GLN G 24 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099038 restraints weight = 14978.499| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 0.76 r_work: 0.3058 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.0405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12746 Z= 0.183 Angle : 0.669 6.166 18453 Z= 0.404 Chirality : 0.052 0.232 2098 Planarity : 0.004 0.045 1330 Dihedral : 29.353 175.152 4040 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.39 % Allowed : 19.75 % Favored : 77.87 % 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: 2.44 (0.31), residues: 741 helix: 2.85 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.63 (0.33), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 20 TYR 0.010 0.001 TYR D 121 PHE 0.010 0.002 PHE E 67 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.18 (12746) covalent geometry : angle 0.66928 / 0.40 (18453) hydrogen bonds : bond 0.07964 / 5.36 ( 756) hydrogen bonds : angle 2.89468 / 2.12 ( 1874) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.310 Fit side-chains REVERT: D 59 MET cc_start: 0.8037 (tpp) cc_final: 0.7699 (tpt) REVERT: D 84 ASN cc_start: 0.8321 (m-40) cc_final: 0.8109 (m-40) REVERT: D 85 LYS cc_start: 0.8515 (mmtp) cc_final: 0.8239 (mttp) REVERT: F 79 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8286 (mmtp) REVERT: G 62 ILE cc_start: 0.8237 (mt) cc_final: 0.8011 (tt) REVERT: G 99 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7919 (mmtm) REVERT: H 47 GLN cc_start: 0.8128 (mt0) cc_final: 0.7916 (mt0) REVERT: H 62 MET cc_start: 0.8454 (mmp) cc_final: 0.7992 (mmm) outliers start: 15 outliers final: 8 residues processed: 166 average time/residue: 0.8279 time to fit residues: 145.0515 Evaluate side-chains 167 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 9 optimal weight: 0.1980 chunk 95 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN G 24 GLN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100103 restraints weight = 15101.718| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 0.75 r_work: 0.3072 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.0505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12746 Z= 0.171 Angle : 0.636 6.377 18453 Z= 0.387 Chirality : 0.050 0.225 2098 Planarity : 0.004 0.041 1330 Dihedral : 29.471 175.995 4018 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.18 % Allowed : 19.11 % Favored : 77.71 % 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: 2.56 (0.31), residues: 741 helix: 2.93 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.56 (0.33), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 129 TYR 0.011 0.001 TYR D 121 PHE 0.010 0.002 PHE E 67 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.17 (12746) covalent geometry : angle 0.63644 / 0.39 (18453) hydrogen bonds : bond 0.07454 / 5.02 ( 756) hydrogen bonds : angle 2.81249 / 2.06 ( 1874) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.231 Fit side-chains REVERT: A 131 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7051 (mtp180) REVERT: D 84 ASN cc_start: 0.8282 (m-40) cc_final: 0.8081 (m-40) REVERT: D 85 LYS cc_start: 0.8485 (mmtp) cc_final: 0.8218 (mttp) REVERT: F 77 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8178 (mttp) REVERT: F 79 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8277 (mmtp) REVERT: G 13 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.7059 (tmtm) REVERT: G 62 ILE cc_start: 0.8204 (mt) cc_final: 0.7986 (tt) REVERT: G 99 LYS cc_start: 0.8135 (mmtm) cc_final: 0.7920 (mmtm) REVERT: H 47 GLN cc_start: 0.8124 (mt0) cc_final: 0.7902 (mt0) REVERT: H 62 MET cc_start: 0.8437 (mmp) cc_final: 0.7990 (mmm) REVERT: H 116 LYS cc_start: 0.8567 (ttpp) cc_final: 0.8361 (ttpp) outliers start: 20 outliers final: 11 residues processed: 173 average time/residue: 0.7676 time to fit residues: 140.3837 Evaluate side-chains 175 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 91 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 59 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.110177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.097738 restraints weight = 14950.481| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 0.74 r_work: 0.3032 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.0579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12746 Z= 0.208 Angle : 0.687 7.225 18453 Z= 0.407 Chirality : 0.054 0.223 2098 Planarity : 0.005 0.047 1330 Dihedral : 29.561 176.298 4017 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.14 % Allowed : 18.31 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.31), residues: 741 helix: 2.76 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.61 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 40 TYR 0.014 0.002 TYR D 121 PHE 0.011 0.002 PHE D 65 HIS 0.007 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.21 (12746) covalent geometry : angle 0.68706 / 0.41 (18453) hydrogen bonds : bond 0.08557 / 5.76 ( 756) hydrogen bonds : angle 2.93589 / 2.16 ( 1874) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.310 Fit side-chains REVERT: A 131 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7117 (mtp180) REVERT: D 85 LYS cc_start: 0.8552 (mmtp) cc_final: 0.8330 (mttp) REVERT: F 77 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8242 (mttp) REVERT: F 79 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8296 (mmtp) REVERT: G 13 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7069 (tmtm) REVERT: G 62 ILE cc_start: 0.8265 (mt) cc_final: 0.8010 (tt) REVERT: G 99 LYS cc_start: 0.8145 (mmtm) cc_final: 0.7930 (mmtm) REVERT: H 47 GLN cc_start: 0.8152 (mt0) cc_final: 0.7929 (mt0) REVERT: H 62 MET cc_start: 0.8485 (mmp) cc_final: 0.8072 (mmm) outliers start: 26 outliers final: 16 residues processed: 160 average time/residue: 0.7417 time to fit residues: 125.3095 Evaluate side-chains 170 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 93 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.110533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098094 restraints weight = 15007.286| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 0.75 r_work: 0.3037 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.0594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12746 Z= 0.190 Angle : 0.676 7.298 18453 Z= 0.402 Chirality : 0.053 0.223 2098 Planarity : 0.005 0.051 1330 Dihedral : 29.568 176.380 4017 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.46 % Allowed : 18.79 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.31), residues: 741 helix: 2.73 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.56 (0.33), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 79 TYR 0.013 0.002 TYR D 121 PHE 0.011 0.002 PHE E 67 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.19 (12746) covalent geometry : angle 0.67570 / 0.40 (18453) hydrogen bonds : bond 0.08416 / 5.67 ( 756) hydrogen bonds : angle 2.92944 / 2.15 ( 1874) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.294 Fit side-chains REVERT: A 131 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7108 (mtp180) REVERT: B 95 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7815 (mtt-85) REVERT: D 85 LYS cc_start: 0.8546 (mmtp) cc_final: 0.8326 (mttp) REVERT: E 120 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.7940 (mtt) REVERT: F 77 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8236 (mttp) REVERT: F 79 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8295 (mmtp) REVERT: G 13 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7064 (tmtm) REVERT: G 62 ILE cc_start: 0.8258 (mt) cc_final: 0.8006 (tt) REVERT: G 99 LYS cc_start: 0.8147 (mmtm) cc_final: 0.7937 (mmtm) REVERT: H 47 GLN cc_start: 0.8153 (mt0) cc_final: 0.7923 (mt0) REVERT: H 62 MET cc_start: 0.8479 (mmp) cc_final: 0.8085 (mmm) outliers start: 28 outliers final: 17 residues processed: 166 average time/residue: 0.8187 time to fit residues: 143.3526 Evaluate side-chains 176 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 91 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 54 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 0.0030 chunk 4 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 38 optimal weight: 0.0040 chunk 19 optimal weight: 1.9990 overall best weight: 0.6204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.099000 restraints weight = 15045.608| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 0.76 r_work: 0.3051 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.0599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12746 Z= 0.161 Angle : 0.650 7.232 18453 Z= 0.391 Chirality : 0.051 0.228 2098 Planarity : 0.004 0.046 1330 Dihedral : 29.581 176.388 4017 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 4.94 % Allowed : 18.15 % Favored : 76.91 % 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: 2.41 (0.31), residues: 741 helix: 2.79 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.51 (0.33), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 129 TYR 0.009 0.001 TYR D 121 PHE 0.011 0.001 PHE E 67 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.16 (12746) covalent geometry : angle 0.65026 / 0.39 (18453) hydrogen bonds : bond 0.07896 / 5.33 ( 756) hydrogen bonds : angle 2.91517 / 2.14 ( 1874) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.199 Fit side-chains REVERT: A 131 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7121 (mtp180) REVERT: B 92 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8089 (ttp80) REVERT: B 95 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7807 (mtt-85) REVERT: D 59 MET cc_start: 0.8076 (tpp) cc_final: 0.7713 (tpt) REVERT: D 85 LYS cc_start: 0.8523 (mmtp) cc_final: 0.8303 (mttp) REVERT: E 120 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.7918 (mtt) REVERT: F 77 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8234 (mttp) REVERT: F 79 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8274 (mmtp) REVERT: G 13 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.7063 (tmtm) REVERT: G 62 ILE cc_start: 0.8220 (mt) cc_final: 0.7990 (tt) REVERT: G 99 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7933 (mmtm) REVERT: H 47 GLN cc_start: 0.8142 (mt0) cc_final: 0.7912 (mt0) REVERT: H 62 MET cc_start: 0.8472 (mmp) cc_final: 0.8169 (mmm) outliers start: 31 outliers final: 18 residues processed: 169 average time/residue: 0.7076 time to fit residues: 126.1459 Evaluate side-chains 181 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 91 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 74 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.0970 chunk 91 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN C 24 GLN G 24 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096590 restraints weight = 15279.217| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 0.79 r_work: 0.3010 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.0665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12746 Z= 0.224 Angle : 0.709 7.829 18453 Z= 0.416 Chirality : 0.055 0.223 2098 Planarity : 0.005 0.050 1330 Dihedral : 29.601 176.355 4017 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.14 % Allowed : 18.79 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.31), residues: 741 helix: 2.66 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.61 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 129 TYR 0.015 0.002 TYR D 121 PHE 0.012 0.002 PHE D 65 HIS 0.007 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.22 (12746) covalent geometry : angle 0.70856 / 0.42 (18453) hydrogen bonds : bond 0.08935 / 6.01 ( 756) hydrogen bonds : angle 2.97559 / 2.18 ( 1874) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.244 Fit side-chains REVERT: A 131 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7110 (mtp180) REVERT: B 95 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7847 (mtt-85) REVERT: D 85 LYS cc_start: 0.8537 (mmtp) cc_final: 0.8320 (mttp) REVERT: F 77 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8285 (mttp) REVERT: F 79 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8325 (mmtp) REVERT: G 62 ILE cc_start: 0.8314 (mt) cc_final: 0.8030 (tt) REVERT: G 64 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: G 99 LYS cc_start: 0.8172 (mmtm) cc_final: 0.7966 (mmtm) REVERT: H 47 GLN cc_start: 0.8203 (mt0) cc_final: 0.7977 (mt0) REVERT: H 62 MET cc_start: 0.8514 (mmp) cc_final: 0.8237 (mmm) outliers start: 26 outliers final: 14 residues processed: 162 average time/residue: 0.7047 time to fit residues: 120.7059 Evaluate side-chains 170 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 91 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 0.0570 chunk 11 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.097929 restraints weight = 15225.009| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 0.78 r_work: 0.3032 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.0649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12746 Z= 0.168 Angle : 0.666 7.707 18453 Z= 0.398 Chirality : 0.051 0.233 2098 Planarity : 0.004 0.048 1330 Dihedral : 29.618 176.518 4013 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.66 % Allowed : 20.22 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.31), residues: 741 helix: 2.74 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.53 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 129 TYR 0.010 0.001 TYR D 121 PHE 0.010 0.002 PHE D 65 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.17 (12746) covalent geometry : angle 0.66601 / 0.40 (18453) hydrogen bonds : bond 0.08160 / 5.51 ( 756) hydrogen bonds : angle 2.95196 / 2.17 ( 1874) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.298 Fit side-chains REVERT: A 131 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7073 (mtp180) REVERT: B 78 ARG cc_start: 0.8565 (mtm110) cc_final: 0.8121 (mtm110) REVERT: B 95 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7821 (mtt-85) REVERT: D 85 LYS cc_start: 0.8514 (mmtp) cc_final: 0.8302 (mttp) REVERT: E 120 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7941 (mtt) REVERT: F 77 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8269 (mttp) REVERT: F 79 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8290 (mmtp) REVERT: G 13 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7079 (tmtm) REVERT: G 62 ILE cc_start: 0.8243 (mt) cc_final: 0.7995 (tt) REVERT: G 99 LYS cc_start: 0.8154 (mmtm) cc_final: 0.7940 (mmtm) REVERT: H 47 GLN cc_start: 0.8152 (mt0) cc_final: 0.7932 (mt0) REVERT: H 62 MET cc_start: 0.8495 (mmp) cc_final: 0.8150 (mmm) outliers start: 23 outliers final: 13 residues processed: 165 average time/residue: 0.7291 time to fit residues: 127.2066 Evaluate side-chains 173 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 91 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 58 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 88 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN C 24 GLN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.111228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.097673 restraints weight = 15104.340| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 0.77 r_work: 0.3028 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.0644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12746 Z= 0.191 Angle : 0.673 7.809 18453 Z= 0.399 Chirality : 0.052 0.226 2098 Planarity : 0.004 0.047 1330 Dihedral : 29.624 176.801 4013 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.34 % Allowed : 20.54 % Favored : 76.11 % 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: 2.36 (0.31), residues: 741 helix: 2.76 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.54 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 129 TYR 0.013 0.002 TYR D 121 PHE 0.011 0.002 PHE E 67 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.19 (12746) covalent geometry : angle 0.67277 / 0.40 (18453) hydrogen bonds : bond 0.08305 / 5.59 ( 756) hydrogen bonds : angle 2.89398 / 2.12 ( 1874) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.296 Fit side-chains REVERT: A 131 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7081 (mtp180) REVERT: B 78 ARG cc_start: 0.8568 (mtm110) cc_final: 0.8137 (mtm110) REVERT: B 95 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7833 (mtt-85) REVERT: D 85 LYS cc_start: 0.8525 (mmtp) cc_final: 0.8310 (mttp) REVERT: F 77 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8264 (mttp) REVERT: F 79 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8314 (mmtp) REVERT: G 13 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7081 (tmtm) REVERT: G 62 ILE cc_start: 0.8283 (mt) cc_final: 0.8020 (tt) REVERT: G 99 LYS cc_start: 0.8167 (mmtm) cc_final: 0.7952 (mmtm) REVERT: H 47 GLN cc_start: 0.8152 (mt0) cc_final: 0.7934 (mt0) REVERT: H 62 MET cc_start: 0.8495 (mmp) cc_final: 0.8216 (mmm) outliers start: 21 outliers final: 14 residues processed: 165 average time/residue: 0.7566 time to fit residues: 131.6870 Evaluate side-chains 174 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.0670 chunk 56 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN C 24 GLN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.097734 restraints weight = 15242.967| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 0.78 r_work: 0.3028 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.0647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12746 Z= 0.184 Angle : 0.671 7.871 18453 Z= 0.398 Chirality : 0.052 0.226 2098 Planarity : 0.004 0.047 1330 Dihedral : 29.629 176.762 4013 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.66 % Allowed : 20.22 % Favored : 76.11 % 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: 2.35 (0.31), residues: 741 helix: 2.76 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.54 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 129 TYR 0.013 0.002 TYR D 121 PHE 0.011 0.002 PHE E 67 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.18 (12746) covalent geometry : angle 0.67106 / 0.40 (18453) hydrogen bonds : bond 0.08237 / 5.55 ( 756) hydrogen bonds : angle 2.89375 / 2.12 ( 1874) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1482 Ramachandran restraints generated. 741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.191 Fit side-chains REVERT: A 131 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7079 (mtp180) REVERT: B 78 ARG cc_start: 0.8565 (mtm110) cc_final: 0.8141 (mtm110) REVERT: B 95 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7830 (mtt-85) REVERT: D 85 LYS cc_start: 0.8524 (mmtp) cc_final: 0.8310 (mttp) REVERT: E 120 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.7937 (mtt) REVERT: F 77 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8265 (mttp) REVERT: F 79 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8314 (mmtp) REVERT: G 13 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7083 (tmtm) REVERT: G 62 ILE cc_start: 0.8277 (mt) cc_final: 0.8012 (tt) REVERT: G 64 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: G 99 LYS cc_start: 0.8165 (mmtm) cc_final: 0.7951 (mmtm) REVERT: H 47 GLN cc_start: 0.8154 (mt0) cc_final: 0.7936 (mt0) REVERT: H 62 MET cc_start: 0.8494 (mmp) cc_final: 0.8215 (mmm) outliers start: 23 outliers final: 14 residues processed: 166 average time/residue: 0.7043 time to fit residues: 123.3894 Evaluate side-chains 176 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN C 24 GLN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.097954 restraints weight = 15218.867| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 0.79 r_work: 0.3032 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.0647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12746 Z= 0.170 Angle : 0.663 7.874 18453 Z= 0.395 Chirality : 0.051 0.228 2098 Planarity : 0.004 0.047 1330 Dihedral : 29.634 176.735 4013 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.50 % Allowed : 20.38 % Favored : 76.11 % 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: 2.37 (0.31), residues: 741 helix: 2.77 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.53 (0.33), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 129 TYR 0.012 0.001 TYR D 121 PHE 0.011 0.002 PHE E 67 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.17 (12746) covalent geometry : angle 0.66254 / 0.39 (18453) hydrogen bonds : bond 0.08128 / 5.48 ( 756) hydrogen bonds : angle 2.88834 / 2.12 ( 1874) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3698.72 seconds wall clock time: 63 minutes 25.57 seconds (3805.57 seconds total)