Starting phenix.real_space_refine on Fri Jul 3 06:21:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8txw_41707/07_2026/8txw_41707.cif Found real_map, /net/cci-nas-00/data/ceres_data/8txw_41707/07_2026/8txw_41707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8txw_41707/07_2026/8txw_41707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8txw_41707/07_2026/8txw_41707.map" model { file = "/net/cci-nas-00/data/ceres_data/8txw_41707/07_2026/8txw_41707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8txw_41707/07_2026/8txw_41707.cif" } resolution = 3.6 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 15 5.16 5 C 7144 2.51 5 N 2407 2.21 5 O 2975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 12835 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 117 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "M" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Time building chain proxies: 2.79, per 1000 atoms: 0.22 Number of scatterers: 12835 At special positions: 0 Unit cell: (103.584, 124.832, 119.52, 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 15 16.00 P 294 15.00 O 2975 8.00 N 2407 7.00 C 7144 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 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 396.5 milliseconds 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1600 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 11 sheets defined 67.6% alpha, 4.2% beta 135 base pairs and 242 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.534A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.814A 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 76 removed outlier: 3.768A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.516A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.559A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.618A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.741A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 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: 3.876A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.624A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.737A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.681A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 37 through 41 Processing helix chain 'M' and resid 55 through 60 removed outlier: 4.482A pdb=" N TYR M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.987A 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 97 removed outlier: 6.767A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.509A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.124A 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 'F' and resid 97 through 98 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.395A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'M' and resid 12 through 16 removed outlier: 9.254A pdb=" N LEU M 67 " --> pdb=" O GLN M 2 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N PHE M 4 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU M 69 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS M 6 " --> pdb=" O LEU M 69 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS M 68 " --> pdb=" O ILE M 44 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 692 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 242 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2641 1.33 - 1.45: 4217 1.45 - 1.57: 6188 1.57 - 1.69: 586 1.69 - 1.81: 26 Bond restraints: 13658 Sorted by residual: bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DA J -68 " pdb=" C2' DA J -68 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DG J 63 " pdb=" C2' DG J 63 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DT J -23 " pdb=" C2' DT J -23 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.74e+00 bond pdb=" C3' DC I 21 " pdb=" C2' DC I 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.63e+00 ... (remaining 13653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 18184 1.33 - 2.66: 1406 2.66 - 3.99: 89 3.99 - 5.31: 13 5.31 - 6.64: 4 Bond angle restraints: 19696 Sorted by residual: angle pdb=" O4' DG J 12 " pdb=" C4' DG J 12 " pdb=" C3' DG J 12 " ideal model delta sigma weight residual 106.00 102.95 3.05 6.00e-01 2.78e+00 2.58e+01 angle pdb=" O4' DG I 26 " pdb=" C4' DG I 26 " pdb=" C3' DG I 26 " ideal model delta sigma weight residual 106.00 103.25 2.75 6.00e-01 2.78e+00 2.09e+01 angle pdb=" N3 DT I 1 " pdb=" C4 DT I 1 " pdb=" O4 DT I 1 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT I -65 " pdb=" C4 DT I -65 " pdb=" O4 DT I -65 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 ... (remaining 19691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.97: 5849 29.97 - 59.94: 1585 59.94 - 89.91: 60 89.91 - 119.88: 0 119.88 - 149.84: 2 Dihedral angle restraints: 7496 sinusoidal: 5011 harmonic: 2485 Sorted by residual: dihedral pdb=" CA LYS G 15 " pdb=" C LYS G 15 " pdb=" N THR G 16 " pdb=" CA THR G 16 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+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 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 70.16 149.84 1 3.50e+01 8.16e-04 1.46e+01 ... (remaining 7493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1334 0.031 - 0.062: 573 0.062 - 0.094: 217 0.094 - 0.125: 111 0.125 - 0.156: 5 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.07e-01 chirality pdb=" CA GLU H 93 " pdb=" N GLU H 93 " pdb=" C GLU H 93 " pdb=" CB GLU H 93 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CB ILE M 36 " pdb=" CA ILE M 36 " pdb=" CG1 ILE M 36 " pdb=" CG2 ILE M 36 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 2237 not shown) Planarity restraints: 1479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 88 " 0.016 2.00e-02 2.50e+03 2.12e-02 8.95e+00 pdb=" CG TYR F 88 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR F 88 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR F 88 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR F 88 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 88 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR F 88 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 88 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 83 " 0.007 2.00e-02 2.50e+03 1.60e-02 5.11e+00 pdb=" CG TYR H 83 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR H 83 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR H 83 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR H 83 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR H 83 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR H 83 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 83 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 83 " 0.017 2.00e-02 2.50e+03 1.15e-02 2.66e+00 pdb=" CG TYR D 83 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR D 83 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR D 83 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 83 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 83 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 83 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR D 83 " 0.001 2.00e-02 2.50e+03 ... (remaining 1476 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 378 2.68 - 3.23: 11120 3.23 - 3.79: 23326 3.79 - 4.34: 29080 4.34 - 4.90: 42063 Nonbonded interactions: 105967 Sorted by model distance: nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.123 2.496 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR M 22 " pdb=" OD1 ASN M 25 " model vdw 2.258 3.040 nonbonded pdb=" NZ LYS B 79 " pdb=" OP1 DG J 27 " model vdw 2.266 3.120 nonbonded pdb=" OE2 GLU A 94 " pdb=" N GLN G 104 " model vdw 2.270 3.120 ... (remaining 105962 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' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.310 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 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 13660 Z= 0.504 Angle : 0.705 6.643 19702 Z= 0.630 Chirality : 0.043 0.156 2240 Planarity : 0.004 0.038 1477 Dihedral : 26.877 149.845 5890 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.14 % Allowed : 0.00 % Favored : 99.86 % 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: 2.65 (0.29), residues: 839 helix: 2.90 (0.22), residues: 545 sheet: 0.77 (1.24), residues: 20 loop : -0.61 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 23 TYR 0.052 0.002 TYR F 88 PHE 0.007 0.001 PHE A 67 HIS 0.005 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.50 (13658) covalent geometry : angle 0.70551 / 0.63 (19696) hydrogen bonds : bond 0.11703 / 7.79 ( 773) hydrogen bonds : angle 3.88105 / 2.73 ( 1929) link_TRANS : bond 0.00160 / 0.08 ( 2) link_TRANS : angle 0.39496 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 110 CYS cc_start: 0.8593 (t) cc_final: 0.7673 (t) REVERT: A 123 ASP cc_start: 0.9036 (m-30) cc_final: 0.8103 (m-30) REVERT: D 71 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8247 (tm-30) REVERT: E 80 THR cc_start: 0.8950 (t) cc_final: 0.8574 (p) REVERT: E 123 ASP cc_start: 0.9098 (m-30) cc_final: 0.8839 (m-30) REVERT: E 129 ARG cc_start: 0.8547 (tpt90) cc_final: 0.8099 (tpt90) REVERT: F 85 ASP cc_start: 0.8813 (m-30) cc_final: 0.8560 (m-30) REVERT: H 85 LYS cc_start: 0.9321 (mttm) cc_final: 0.9035 (mmtt) REVERT: H 99 ARG cc_start: 0.8516 (mtt-85) cc_final: 0.8278 (mtm-85) REVERT: H 120 LYS cc_start: 0.9214 (tttm) cc_final: 0.9008 (tttp) REVERT: C 40 SER cc_start: 0.8899 (t) cc_final: 0.8695 (t) REVERT: C 95 LYS cc_start: 0.9191 (tptm) cc_final: 0.8813 (ttmm) REVERT: G 41 GLU cc_start: 0.8591 (tp30) cc_final: 0.8376 (tp30) REVERT: G 64 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8416 (tm-30) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1590 time to fit residues: 37.5344 Evaluate side-chains 152 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.104925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.068123 restraints weight = 47938.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.070892 restraints weight = 19329.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.072593 restraints weight = 11929.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.073780 restraints weight = 9307.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.074303 restraints weight = 8152.617| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13660 Z= 0.164 Angle : 0.597 7.020 19702 Z= 0.366 Chirality : 0.042 0.203 2240 Planarity : 0.004 0.036 1477 Dihedral : 29.940 153.812 4170 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.97 % Allowed : 7.91 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.30), residues: 839 helix: 2.84 (0.22), residues: 560 sheet: 0.35 (1.20), residues: 20 loop : -0.63 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 23 TYR 0.039 0.002 TYR F 88 PHE 0.009 0.001 PHE H 70 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.16 (13658) covalent geometry : angle 0.59746 / 0.37 (19696) hydrogen bonds : bond 0.05482 / 3.53 ( 773) hydrogen bonds : angle 3.25568 / 2.27 ( 1929) link_TRANS : bond 0.00074 / 0.04 ( 2) link_TRANS : angle 0.41596 / 0.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 158 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 110 CYS cc_start: 0.8466 (t) cc_final: 0.7805 (t) REVERT: A 123 ASP cc_start: 0.8999 (m-30) cc_final: 0.8319 (m-30) REVERT: D 71 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8188 (tm-30) REVERT: E 120 MET cc_start: 0.8338 (mtt) cc_final: 0.8081 (mtt) REVERT: E 129 ARG cc_start: 0.8530 (tpt90) cc_final: 0.8161 (tpt90) REVERT: H 68 ASP cc_start: 0.8931 (t0) cc_final: 0.8719 (t0) REVERT: C 99 ARG cc_start: 0.8231 (mmt180) cc_final: 0.8018 (mmt180) REVERT: G 64 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8537 (tm-30) outliers start: 6 outliers final: 6 residues processed: 161 average time/residue: 0.1489 time to fit residues: 32.0021 Evaluate side-chains 154 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 49 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 47 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 97 optimal weight: 0.0040 chunk 104 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.104447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.067228 restraints weight = 53225.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.070014 restraints weight = 20421.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.072000 restraints weight = 12367.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.073057 restraints weight = 9459.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.073670 restraints weight = 8261.808| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13660 Z= 0.163 Angle : 0.588 7.654 19702 Z= 0.355 Chirality : 0.041 0.183 2240 Planarity : 0.004 0.034 1477 Dihedral : 30.061 154.247 4170 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.97 % Allowed : 11.93 % Favored : 87.10 % 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: 2.59 (0.29), residues: 839 helix: 2.83 (0.22), residues: 561 sheet: 0.24 (1.18), residues: 20 loop : -0.79 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 23 TYR 0.035 0.002 TYR F 88 PHE 0.007 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (13658) covalent geometry : angle 0.58756 / 0.36 (19696) hydrogen bonds : bond 0.05152 / 3.35 ( 773) hydrogen bonds : angle 3.11178 / 2.17 ( 1929) link_TRANS : bond 0.00081 / 0.04 ( 2) link_TRANS : angle 0.33219 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 156 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8741 (pm20) cc_final: 0.8538 (pm20) REVERT: A 110 CYS cc_start: 0.8489 (t) cc_final: 0.7868 (t) REVERT: A 123 ASP cc_start: 0.9038 (m-30) cc_final: 0.8426 (m-30) REVERT: D 71 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8213 (tm-30) REVERT: E 129 ARG cc_start: 0.8558 (tpt90) cc_final: 0.8163 (tpt90) REVERT: G 64 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8512 (tt0) outliers start: 6 outliers final: 5 residues processed: 158 average time/residue: 0.1522 time to fit residues: 32.3571 Evaluate side-chains 156 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 151 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 71 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 80 optimal weight: 0.3980 chunk 76 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 93 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.103546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.067210 restraints weight = 60432.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.070300 restraints weight = 22259.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.071185 restraints weight = 14101.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.071822 restraints weight = 9748.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.072190 restraints weight = 8999.106| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13660 Z= 0.176 Angle : 0.599 7.624 19702 Z= 0.357 Chirality : 0.041 0.186 2240 Planarity : 0.004 0.034 1477 Dihedral : 30.175 155.337 4170 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.39 % Allowed : 13.87 % Favored : 84.74 % 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: 2.57 (0.29), residues: 839 helix: 2.82 (0.22), residues: 560 sheet: 0.39 (1.19), residues: 20 loop : -0.80 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 67 TYR 0.032 0.002 TYR F 88 PHE 0.008 0.001 PHE A 67 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.18 (13658) covalent geometry : angle 0.59939 / 0.36 (19696) hydrogen bonds : bond 0.05219 / 3.40 ( 773) hydrogen bonds : angle 3.09488 / 2.16 ( 1929) link_TRANS : bond 0.00055 / 0.03 ( 2) link_TRANS : angle 0.35052 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 CYS cc_start: 0.8403 (t) cc_final: 0.7946 (t) REVERT: A 123 ASP cc_start: 0.9089 (m-30) cc_final: 0.8365 (m-30) REVERT: B 88 TYR cc_start: 0.7865 (m-10) cc_final: 0.7567 (m-10) REVERT: E 129 ARG cc_start: 0.8601 (tpt90) cc_final: 0.8205 (tpt90) REVERT: F 25 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8582 (m-40) outliers start: 9 outliers final: 7 residues processed: 155 average time/residue: 0.1503 time to fit residues: 31.4679 Evaluate side-chains 159 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 40 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN F 25 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.102237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.065062 restraints weight = 44040.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.067598 restraints weight = 19112.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.069337 restraints weight = 12285.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.070247 restraints weight = 9720.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.070675 restraints weight = 8657.729| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 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 : 0.005 0.083 13660 Z= 0.218 Angle : 0.631 8.248 19702 Z= 0.368 Chirality : 0.042 0.200 2240 Planarity : 0.004 0.033 1477 Dihedral : 30.286 155.926 4170 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.08 % Allowed : 15.26 % Favored : 82.66 % 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: 2.48 (0.29), residues: 839 helix: 2.76 (0.22), residues: 560 sheet: 0.42 (1.20), residues: 20 loop : -0.89 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 23 TYR 0.026 0.002 TYR F 88 PHE 0.009 0.002 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.22 (13658) covalent geometry : angle 0.63150 / 0.37 (19696) hydrogen bonds : bond 0.05513 / 3.61 ( 773) hydrogen bonds : angle 3.18534 / 2.23 ( 1929) link_TRANS : bond 0.00086 / 0.04 ( 2) link_TRANS : angle 0.46736 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8255 (m-10) cc_final: 0.7961 (m-10) REVERT: E 129 ARG cc_start: 0.8584 (tpt90) cc_final: 0.8189 (tpt90) REVERT: F 25 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8269 (m110) REVERT: G 64 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8814 (tm-30) outliers start: 14 outliers final: 12 residues processed: 156 average time/residue: 0.1368 time to fit residues: 28.9579 Evaluate side-chains 160 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 40 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 0.0000 chunk 86 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN F 25 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.103374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.067339 restraints weight = 58647.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.070282 restraints weight = 21882.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.071127 restraints weight = 13972.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.071766 restraints weight = 9794.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.071789 restraints weight = 8934.403| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13660 Z= 0.160 Angle : 0.594 8.971 19702 Z= 0.354 Chirality : 0.041 0.187 2240 Planarity : 0.004 0.034 1477 Dihedral : 30.225 155.371 4170 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.80 % Allowed : 15.95 % Favored : 82.25 % 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: 2.50 (0.29), residues: 839 helix: 2.79 (0.22), residues: 560 sheet: 0.51 (1.21), residues: 20 loop : -0.91 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 23 TYR 0.023 0.002 TYR F 88 PHE 0.007 0.001 PHE A 67 HIS 0.002 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 (13658) covalent geometry : angle 0.59418 / 0.35 (19696) hydrogen bonds : bond 0.05057 / 3.28 ( 773) hydrogen bonds : angle 3.03183 / 2.11 ( 1929) link_TRANS : bond 0.00061 / 0.03 ( 2) link_TRANS : angle 0.30758 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8699 (pm20) cc_final: 0.8334 (pm20) REVERT: E 129 ARG cc_start: 0.8581 (tpt90) cc_final: 0.8190 (tpt90) REVERT: F 25 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8108 (m-40) REVERT: G 64 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8766 (tm-30) outliers start: 12 outliers final: 10 residues processed: 158 average time/residue: 0.1327 time to fit residues: 28.8955 Evaluate side-chains 160 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain C residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN B 93 GLN F 25 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.104059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.068248 restraints weight = 54999.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.071355 restraints weight = 21101.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.072064 restraints weight = 13530.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.072486 restraints weight = 9488.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.072774 restraints weight = 8870.642| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13660 Z= 0.148 Angle : 0.581 9.209 19702 Z= 0.348 Chirality : 0.040 0.185 2240 Planarity : 0.004 0.034 1477 Dihedral : 30.175 155.538 4170 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.80 % Allowed : 16.50 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.29), residues: 839 helix: 2.84 (0.22), residues: 560 sheet: 0.56 (1.22), residues: 20 loop : -0.90 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.019 0.002 TYR F 88 PHE 0.007 0.001 PHE E 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.15 (13658) covalent geometry : angle 0.58155 / 0.35 (19696) hydrogen bonds : bond 0.04845 / 3.14 ( 773) hydrogen bonds : angle 2.94948 / 2.05 ( 1929) link_TRANS : bond 0.00048 / 0.02 ( 2) link_TRANS : angle 0.28926 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8711 (pm20) cc_final: 0.8312 (pm20) REVERT: E 129 ARG cc_start: 0.8568 (tpt90) cc_final: 0.8193 (tpt90) REVERT: F 25 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8152 (m110) REVERT: G 64 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8775 (tm-30) outliers start: 12 outliers final: 9 residues processed: 157 average time/residue: 0.1302 time to fit residues: 27.9832 Evaluate side-chains 157 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain C residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 11 optimal weight: 0.5980 chunk 90 optimal weight: 0.3980 chunk 52 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.104236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.066932 restraints weight = 52751.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.069725 restraints weight = 20731.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.071556 restraints weight = 12661.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.072591 restraints weight = 9768.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.073067 restraints weight = 8579.542| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13660 Z= 0.150 Angle : 0.581 9.357 19702 Z= 0.348 Chirality : 0.040 0.186 2240 Planarity : 0.004 0.034 1477 Dihedral : 30.162 155.857 4170 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.27 % Favored : 97.61 % Rotamer: Outliers : 1.80 % Allowed : 17.61 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.29), residues: 839 helix: 2.83 (0.22), residues: 560 sheet: 0.60 (1.23), residues: 20 loop : -0.89 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.019 0.002 TYR F 88 PHE 0.007 0.001 PHE A 67 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (13658) covalent geometry : angle 0.58139 / 0.35 (19696) hydrogen bonds : bond 0.04788 / 3.10 ( 773) hydrogen bonds : angle 2.92641 / 2.03 ( 1929) link_TRANS : bond 0.00036 / 0.02 ( 2) link_TRANS : angle 0.28615 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8675 (pm20) cc_final: 0.8274 (pm20) REVERT: E 129 ARG cc_start: 0.8555 (tpt90) cc_final: 0.8192 (tpt90) REVERT: G 64 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8774 (tm-30) outliers start: 12 outliers final: 9 residues processed: 151 average time/residue: 0.1250 time to fit residues: 25.8036 Evaluate side-chains 156 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain C residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 11 optimal weight: 0.3980 chunk 81 optimal weight: 9.9990 chunk 105 optimal weight: 0.0970 chunk 59 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 84 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.105186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.068866 restraints weight = 38011.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.071344 restraints weight = 17099.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.073087 restraints weight = 11225.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.073969 restraints weight = 8979.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.074391 restraints weight = 8045.452| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13660 Z= 0.141 Angle : 0.569 9.425 19702 Z= 0.343 Chirality : 0.039 0.193 2240 Planarity : 0.004 0.034 1477 Dihedral : 30.125 156.029 4170 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.39 % Favored : 97.49 % Rotamer: Outliers : 1.25 % Allowed : 17.75 % Favored : 81.00 % 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: 2.61 (0.30), residues: 839 helix: 2.85 (0.22), residues: 562 sheet: 0.67 (1.23), residues: 20 loop : -0.85 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.019 0.001 TYR C 39 PHE 0.006 0.001 PHE A 78 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.14 (13658) covalent geometry : angle 0.56913 / 0.34 (19696) hydrogen bonds : bond 0.04552 / 2.93 ( 773) hydrogen bonds : angle 2.86548 / 1.98 ( 1929) link_TRANS : bond 0.00066 / 0.03 ( 2) link_TRANS : angle 0.24457 / 0.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8693 (pm20) cc_final: 0.8269 (pm20) REVERT: A 123 ASP cc_start: 0.8819 (m-30) cc_final: 0.8430 (m-30) REVERT: B 88 TYR cc_start: 0.7087 (m-80) cc_final: 0.6716 (m-80) REVERT: E 129 ARG cc_start: 0.8561 (tpt90) cc_final: 0.8193 (tpt90) REVERT: G 64 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8781 (tm-30) outliers start: 8 outliers final: 7 residues processed: 155 average time/residue: 0.1248 time to fit residues: 26.6271 Evaluate side-chains 155 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain C residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.104726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.067779 restraints weight = 48104.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.070458 restraints weight = 19813.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.072286 restraints weight = 12299.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.073262 restraints weight = 9590.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.073885 restraints weight = 8467.729| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 13660 Z= 0.160 Angle : 0.592 9.460 19702 Z= 0.350 Chirality : 0.040 0.190 2240 Planarity : 0.004 0.034 1477 Dihedral : 30.166 156.510 4170 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.27 % Favored : 97.61 % Rotamer: Outliers : 1.39 % Allowed : 17.89 % Favored : 80.72 % 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: 2.55 (0.30), residues: 839 helix: 2.80 (0.22), residues: 562 sheet: 0.68 (1.24), residues: 20 loop : -0.88 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 23 TYR 0.027 0.002 TYR D 83 PHE 0.006 0.001 PHE A 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (13658) covalent geometry : angle 0.59196 / 0.35 (19696) hydrogen bonds : bond 0.04706 / 3.06 ( 773) hydrogen bonds : angle 2.91368 / 2.03 ( 1929) link_TRANS : bond 0.00021 / 0.01 ( 2) link_TRANS : angle 0.28156 / 0.12 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8684 (pm20) cc_final: 0.8277 (pm20) REVERT: D 83 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.6870 (t80) REVERT: E 129 ARG cc_start: 0.8548 (tpt90) cc_final: 0.8187 (tpt90) REVERT: G 64 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8636 (tm-30) outliers start: 9 outliers final: 7 residues processed: 153 average time/residue: 0.1406 time to fit residues: 29.4167 Evaluate side-chains 155 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain C residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 70 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 105 optimal weight: 0.3980 chunk 101 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.104490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.068374 restraints weight = 34647.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.070705 restraints weight = 16646.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.072337 restraints weight = 11276.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.073144 restraints weight = 9183.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.073554 restraints weight = 8303.486| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13660 Z= 0.160 Angle : 0.592 9.659 19702 Z= 0.350 Chirality : 0.040 0.193 2240 Planarity : 0.004 0.034 1477 Dihedral : 30.196 156.504 4170 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.39 % Favored : 97.49 % Rotamer: Outliers : 1.39 % Allowed : 17.75 % Favored : 80.86 % 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: 2.55 (0.30), residues: 839 helix: 2.82 (0.22), residues: 560 sheet: 0.70 (1.25), residues: 20 loop : -0.89 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 23 TYR 0.022 0.002 TYR F 88 PHE 0.007 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (13658) covalent geometry : angle 0.59219 / 0.35 (19696) hydrogen bonds : bond 0.04770 / 3.10 ( 773) hydrogen bonds : angle 2.94161 / 2.06 ( 1929) link_TRANS : bond 0.00011 / 0.01 ( 2) link_TRANS : angle 0.27838 / 0.11 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2289.81 seconds wall clock time: 40 minutes 2.52 seconds (2402.52 seconds total)