Starting phenix.real_space_refine on Sat Aug 23 14:06:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8txw_41707/08_2025/8txw_41707.cif Found real_map, /net/cci-nas-00/data/ceres_data/8txw_41707/08_2025/8txw_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_41707/08_2025/8txw_41707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8txw_41707/08_2025/8txw_41707.map" model { file = "/net/cci-nas-00/data/ceres_data/8txw_41707/08_2025/8txw_41707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8txw_41707/08_2025/8txw_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-2.0-5787/lib/python3.9/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: 3.17, per 1000 atoms: 0.25 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: 1.10 Conformation dependent library (CDL) restraints added in 311.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.79 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: 2.33 Time building geometry restraints manager: 1.49 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' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.452 -0.030 3.00e-02 1.11e+03 9.75e-01 bond pdb=" CB GLU H 93 " pdb=" CG GLU H 93 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.54e-01 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.08e-01 bond pdb=" C3' DA J -68 " pdb=" C2' DA J -68 " ideal model delta sigma weight residual 1.525 1.542 -0.017 2.00e-02 2.50e+03 7.45e-01 bond pdb=" C4' DG I 26 " pdb=" C3' DG I 26 " ideal model delta sigma weight residual 1.523 1.506 0.017 2.00e-02 2.50e+03 7.41e-01 ... (remaining 13653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 19008 1.33 - 2.66: 641 2.66 - 3.99: 30 3.99 - 5.31: 13 5.31 - 6.64: 4 Bond angle restraints: 19696 Sorted by residual: angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 121.54 127.95 -6.41 1.91e+00 2.74e-01 1.13e+01 angle pdb=" C GLU K 473 " pdb=" N TYR K 474 " pdb=" CA TYR K 474 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.47e+00 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 113.18 119.82 -6.64 2.37e+00 1.78e-01 7.86e+00 angle pdb=" CA GLU A 105 " pdb=" CB GLU A 105 " pdb=" CG GLU A 105 " ideal model delta sigma weight residual 114.10 118.83 -4.73 2.00e+00 2.50e-01 5.60e+00 angle pdb=" CB MET H 59 " pdb=" CG MET H 59 " pdb=" SD MET H 59 " ideal model delta sigma weight residual 112.70 118.98 -6.28 3.00e+00 1.11e-01 4.39e+00 ... (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: 1617 0.031 - 0.062: 490 0.062 - 0.094: 87 0.094 - 0.125: 42 0.125 - 0.156: 4 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: 1.010 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.090 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 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 : 0.004 0.030 13660 Z= 0.165 Angle : 0.542 6.643 19702 Z= 0.325 Chirality : 0.033 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 aren 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 covalent geometry : bond 0.00359 (13658) covalent geometry : angle 0.54158 (19696) hydrogen bonds : bond 0.11703 ( 773) hydrogen bonds : angle 3.88105 ( 1929) link_TRANS : bond 0.00160 ( 2) link_TRANS : angle 0.39496 ( 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 : 0.265 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: 0.8629 (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: 0.8548 (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: 0.9034 (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: 0.1543 time to fit residues: 36.2075 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 : 0.250 ------------------------------------------------------------------------------- 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: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 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... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** 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 = 0.3582 r_free = 0.3582 target = 0.105040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.068025 restraints weight = 47904.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.070707 restraints weight = 19758.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.072600 restraints weight = 12326.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.073586 restraints weight = 9580.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.074077 restraints weight = 8456.977| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 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 = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13660 Z= 0.170 Angle : 0.552 7.965 19702 Z= 0.330 Chirality : 0.033 0.180 2240 Planarity : 0.004 0.035 1477 Dihedral : 29.636 149.982 4170 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.97 % Allowed : 8.04 % Favored : 90.98 % 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 aren not related in a simple way. whole: 2.71 (0.30), residues: 839 helix: 2.88 (0.22), residues: 561 sheet: 0.42 (1.20), residues: 20 loop : -0.64 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 23 TYR 0.040 0.002 TYR F 88 PHE 0.008 0.001 PHE A 67 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00370 (13658) covalent geometry : angle 0.55183 (19696) hydrogen bonds : bond 0.04646 ( 773) hydrogen bonds : angle 3.14447 ( 1929) link_TRANS : bond 0.00027 ( 2) link_TRANS : angle 0.35557 ( 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 169 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 163 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8708 (pm20) cc_final: 0.8484 (pm20) REVERT: A 110 CYS cc_start: 0.8436 (t) cc_final: 0.7776 (t) REVERT: A 123 ASP cc_start: 0.8985 (m-30) cc_final: 0.8332 (m-30) REVERT: D 71 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8177 (tm-30) REVERT: E 122 LYS cc_start: 0.8861 (ptpp) cc_final: 0.8620 (ptpp) REVERT: E 129 ARG cc_start: 0.8529 (tpt90) cc_final: 0.8160 (tpt90) REVERT: G 64 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8553 (tm-30) outliers start: 6 outliers final: 6 residues processed: 165 average time/residue: 0.1695 time to fit residues: 36.7689 Evaluate side-chains 155 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 47 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN F 25 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.102958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.067448 restraints weight = 53233.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.069849 restraints weight = 22060.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.070842 restraints weight = 14179.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.071336 restraints weight = 9735.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.071372 restraints weight = 8918.646| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13660 Z= 0.218 Angle : 0.576 7.850 19702 Z= 0.342 Chirality : 0.035 0.174 2240 Planarity : 0.004 0.033 1477 Dihedral : 29.734 150.327 4170 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.25 % Allowed : 12.90 % Favored : 85.85 % 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 aren not related in a simple way. whole: 2.58 (0.30), residues: 839 helix: 2.81 (0.22), residues: 560 sheet: 0.21 (1.17), residues: 20 loop : -0.74 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 23 TYR 0.036 0.002 TYR F 88 PHE 0.009 0.001 PHE A 67 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00496 (13658) covalent geometry : angle 0.57637 (19696) hydrogen bonds : bond 0.05071 ( 773) hydrogen bonds : angle 3.14969 ( 1929) link_TRANS : bond 0.00052 ( 2) link_TRANS : angle 0.46910 ( 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 159 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8538 (m-10) cc_final: 0.8293 (m-10) REVERT: D 71 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8174 (tm-30) REVERT: E 129 ARG cc_start: 0.8605 (tpt90) cc_final: 0.8208 (tpt90) outliers start: 8 outliers final: 7 residues processed: 155 average time/residue: 0.1358 time to fit residues: 28.4894 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 : 0.229 ------------------------------------------------------------------------------- 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 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: 0.0060 chunk 97 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 107 optimal weight: 0.1980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 93 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN F 25 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.105690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.069756 restraints weight = 60629.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.072077 restraints weight = 22411.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.073380 restraints weight = 14012.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.074349 restraints weight = 9714.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.074331 restraints weight = 8750.723| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13660 Z= 0.146 Angle : 0.533 8.632 19702 Z= 0.319 Chirality : 0.033 0.180 2240 Planarity : 0.004 0.034 1477 Dihedral : 29.520 149.348 4170 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.97 % Allowed : 14.84 % Favored : 84.19 % 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 aren not related in a simple way. whole: 2.75 (0.30), residues: 839 helix: 2.93 (0.22), residues: 562 sheet: 0.50 (1.19), residues: 20 loop : -0.70 (0.35), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.021 0.001 TYR F 88 PHE 0.008 0.001 PHE E 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00309 (13658) covalent geometry : angle 0.53283 (19696) hydrogen bonds : bond 0.04105 ( 773) hydrogen bonds : angle 2.81603 ( 1929) link_TRANS : bond 0.00080 ( 2) link_TRANS : angle 0.32262 ( 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 163 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 157 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8655 (pm20) cc_final: 0.8393 (pm20) REVERT: A 73 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6980 (mt-10) REVERT: B 88 TYR cc_start: 0.8506 (m-10) cc_final: 0.8165 (m-10) REVERT: E 129 ARG cc_start: 0.8581 (tpt90) cc_final: 0.8218 (tpt90) REVERT: G 64 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8768 (tm-30) outliers start: 6 outliers final: 4 residues processed: 159 average time/residue: 0.1258 time to fit residues: 27.0009 Evaluate side-chains 154 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 150 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.102886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.065607 restraints weight = 43979.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.068122 restraints weight = 19000.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.069868 restraints weight = 12229.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.070787 restraints weight = 9697.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.071299 restraints weight = 8643.110| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13660 Z= 0.208 Angle : 0.567 8.835 19702 Z= 0.337 Chirality : 0.035 0.195 2240 Planarity : 0.004 0.034 1477 Dihedral : 29.747 150.531 4170 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.39 % Favored : 97.49 % Rotamer: Outliers : 1.66 % Allowed : 15.81 % Favored : 82.52 % 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 aren not related in a simple way. whole: 2.63 (0.30), residues: 839 helix: 2.85 (0.22), residues: 560 sheet: 0.47 (1.20), residues: 20 loop : -0.74 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 23 TYR 0.027 0.002 TYR F 88 PHE 0.008 0.001 PHE B 61 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00474 (13658) covalent geometry : angle 0.56732 (19696) hydrogen bonds : bond 0.04914 ( 773) hydrogen bonds : angle 3.02095 ( 1929) link_TRANS : bond 0.00049 ( 2) link_TRANS : angle 0.39224 ( 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 159 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8670 (pm20) cc_final: 0.8337 (pm20) REVERT: A 73 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6348 (mt-10) REVERT: B 88 TYR cc_start: 0.8867 (m-10) cc_final: 0.8323 (m-80) REVERT: E 129 ARG cc_start: 0.8568 (tpt90) cc_final: 0.8185 (tpt90) REVERT: G 64 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8653 (tm-30) outliers start: 11 outliers final: 8 residues processed: 151 average time/residue: 0.1367 time to fit residues: 28.1327 Evaluate side-chains 154 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 120 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 107 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 chunk 86 optimal weight: 30.0000 chunk 78 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 chunk 93 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.105573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.069699 restraints weight = 58697.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.072184 restraints weight = 21435.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.073380 restraints weight = 13972.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.074255 restraints weight = 9503.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.074216 restraints weight = 8499.170| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 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 = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13660 Z= 0.145 Angle : 0.533 9.046 19702 Z= 0.319 Chirality : 0.033 0.201 2240 Planarity : 0.004 0.035 1477 Dihedral : 29.569 149.506 4170 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.03 % Favored : 97.85 % Rotamer: Outliers : 0.97 % Allowed : 15.95 % Favored : 83.08 % 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 aren not related in a simple way. whole: 2.71 (0.29), residues: 839 helix: 2.90 (0.22), residues: 562 sheet: 0.62 (1.22), residues: 20 loop : -0.72 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.019 0.001 TYR C 39 PHE 0.007 0.001 PHE E 67 HIS 0.002 0.000 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00307 (13658) covalent geometry : angle 0.53295 (19696) hydrogen bonds : bond 0.04010 ( 773) hydrogen bonds : angle 2.75119 ( 1929) link_TRANS : bond 0.00066 ( 2) link_TRANS : angle 0.27785 ( 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 158 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 152 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 110 CYS cc_start: 0.8429 (t) cc_final: 0.7779 (t) REVERT: A 123 ASP cc_start: 0.8768 (m-30) cc_final: 0.8084 (m-30) REVERT: B 88 TYR cc_start: 0.8825 (m-10) cc_final: 0.8382 (m-80) REVERT: E 129 ARG cc_start: 0.8569 (tpt90) cc_final: 0.8193 (tpt90) REVERT: G 64 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8782 (tm-30) outliers start: 6 outliers final: 5 residues processed: 155 average time/residue: 0.1407 time to fit residues: 28.9976 Evaluate side-chains 152 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 147 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 30 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 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 = 0.3587 r_free = 0.3587 target = 0.105431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.068042 restraints weight = 55190.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.070877 restraints weight = 20886.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.072844 restraints weight = 12487.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.073912 restraints weight = 9504.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.074576 restraints weight = 8296.749| |-----------------------------------------------------------------------------| 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 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 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 : 0.003 0.031 13660 Z= 0.158 Angle : 0.548 11.285 19702 Z= 0.324 Chirality : 0.033 0.185 2240 Planarity : 0.004 0.035 1477 Dihedral : 29.582 149.969 4170 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.03 % Favored : 97.85 % Rotamer: Outliers : 1.25 % Allowed : 16.09 % 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 aren not related in a simple way. whole: 2.70 (0.29), residues: 839 helix: 2.90 (0.22), residues: 562 sheet: 0.61 (1.21), residues: 20 loop : -0.76 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 23 TYR 0.023 0.002 TYR F 98 PHE 0.006 0.001 PHE E 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00346 (13658) covalent geometry : angle 0.54808 (19696) hydrogen bonds : bond 0.04099 ( 773) hydrogen bonds : angle 2.77985 ( 1929) link_TRANS : bond 0.00018 ( 2) link_TRANS : angle 0.21341 ( 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 160 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8668 (pm20) cc_final: 0.8292 (pm20) REVERT: A 110 CYS cc_start: 0.8453 (t) cc_final: 0.7656 (t) REVERT: A 123 ASP cc_start: 0.8761 (m-30) cc_final: 0.7808 (m-30) REVERT: B 88 TYR cc_start: 0.8879 (m-10) cc_final: 0.8370 (m-80) REVERT: E 129 ARG cc_start: 0.8558 (tpt90) cc_final: 0.8190 (tpt90) REVERT: C 63 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9271 (mt) REVERT: G 64 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8621 (tm-30) outliers start: 8 outliers final: 6 residues processed: 156 average time/residue: 0.1467 time to fit residues: 31.1176 Evaluate side-chains 153 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain C residue 63 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 11 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 52 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 84 optimal weight: 0.0370 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 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 = 0.3593 r_free = 0.3593 target = 0.105866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.068650 restraints weight = 52940.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.071455 restraints weight = 20406.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.073384 restraints weight = 12328.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.074427 restraints weight = 9449.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.074991 restraints weight = 8276.311| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 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 = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13660 Z= 0.148 Angle : 0.544 10.243 19702 Z= 0.322 Chirality : 0.033 0.183 2240 Planarity : 0.004 0.036 1477 Dihedral : 29.589 150.086 4170 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.25 % Allowed : 16.64 % Favored : 82.11 % 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 aren not related in a simple way. whole: 2.72 (0.29), residues: 839 helix: 2.92 (0.22), residues: 562 sheet: 0.62 (1.21), residues: 20 loop : -0.76 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 23 TYR 0.022 0.001 TYR C 39 PHE 0.007 0.001 PHE E 67 HIS 0.002 0.000 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00318 (13658) covalent geometry : angle 0.54447 (19696) hydrogen bonds : bond 0.04044 ( 773) hydrogen bonds : angle 2.74632 ( 1929) link_TRANS : bond 0.00056 ( 2) link_TRANS : angle 0.21873 ( 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 158 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8686 (pm20) cc_final: 0.8302 (pm20) REVERT: A 110 CYS cc_start: 0.8439 (t) cc_final: 0.7636 (t) REVERT: A 123 ASP cc_start: 0.8746 (m-30) cc_final: 0.8050 (m-30) REVERT: B 88 TYR cc_start: 0.8866 (m-10) cc_final: 0.8381 (m-80) REVERT: E 129 ARG cc_start: 0.8555 (tpt90) cc_final: 0.8185 (tpt90) REVERT: F 98 TYR cc_start: 0.9048 (m-10) cc_final: 0.8823 (m-10) REVERT: G 64 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8594 (tm-30) outliers start: 8 outliers final: 7 residues processed: 154 average time/residue: 0.1482 time to fit residues: 30.6909 Evaluate side-chains 154 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 80 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain G residue 15 LYS 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: 2.9990 chunk 68 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 81 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 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 = 0.3550 r_free = 0.3550 target = 0.103334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.066541 restraints weight = 38084.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.068980 restraints weight = 17558.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.070637 restraints weight = 11629.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.071478 restraints weight = 9389.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.071872 restraints weight = 8455.681| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 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 = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13660 Z= 0.203 Angle : 0.578 11.139 19702 Z= 0.339 Chirality : 0.035 0.181 2240 Planarity : 0.004 0.035 1477 Dihedral : 29.752 150.796 4170 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.39 % Favored : 97.37 % Rotamer: Outliers : 1.53 % Allowed : 16.78 % 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 aren not related in a simple way. whole: 2.63 (0.30), residues: 839 helix: 2.89 (0.22), residues: 560 sheet: 0.48 (1.21), residues: 20 loop : -0.85 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 23 TYR 0.028 0.002 TYR F 88 PHE 0.007 0.001 PHE B 61 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00461 (13658) covalent geometry : angle 0.57762 (19696) hydrogen bonds : bond 0.04748 ( 773) hydrogen bonds : angle 2.93816 ( 1929) link_TRANS : bond 0.00051 ( 2) link_TRANS : angle 0.28017 ( 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 157 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7525 (mt-10) REVERT: B 88 TYR cc_start: 0.8923 (m-10) cc_final: 0.8367 (m-80) REVERT: E 129 ARG cc_start: 0.8553 (tpt90) cc_final: 0.8162 (tpt90) REVERT: G 64 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8363 (tm-30) outliers start: 10 outliers final: 9 residues processed: 151 average time/residue: 0.1264 time to fit residues: 25.8343 Evaluate side-chains 154 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 F residue 80 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain G residue 15 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 101 optimal weight: 0.2980 chunk 63 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.104307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.067130 restraints weight = 48193.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.069794 restraints weight = 19843.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.071617 restraints weight = 12360.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.072588 restraints weight = 9649.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.073049 restraints weight = 8539.531| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 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 = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13660 Z= 0.173 Angle : 0.564 11.957 19702 Z= 0.331 Chirality : 0.034 0.177 2240 Planarity : 0.004 0.035 1477 Dihedral : 29.685 150.145 4170 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.39 % Favored : 97.37 % Rotamer: Outliers : 1.11 % Allowed : 16.92 % Favored : 81.97 % 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 aren not related in a simple way. whole: 2.61 (0.29), residues: 839 helix: 2.88 (0.22), residues: 560 sheet: 0.51 (1.21), residues: 20 loop : -0.87 (0.36), 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 E 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00386 (13658) covalent geometry : angle 0.56374 (19696) hydrogen bonds : bond 0.04391 ( 773) hydrogen bonds : angle 2.83981 ( 1929) link_TRANS : bond 0.00012 ( 2) link_TRANS : angle 0.23668 ( 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 155 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9040 (m-30) cc_final: 0.8733 (m-30) REVERT: B 88 TYR cc_start: 0.8889 (m-10) cc_final: 0.8404 (m-80) REVERT: E 129 ARG cc_start: 0.8548 (tpt90) cc_final: 0.8167 (tpt90) REVERT: G 64 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8632 (tm-30) outliers start: 7 outliers final: 7 residues processed: 151 average time/residue: 0.1403 time to fit residues: 28.5262 Evaluate side-chains 152 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 110 CYS 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 40 SER Chi-restraints excluded: chain G residue 15 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.0980 chunk 75 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** 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 = 0.3578 r_free = 0.3578 target = 0.104947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.068714 restraints weight = 34641.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.071183 restraints weight = 16582.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.072629 restraints weight = 11189.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.073347 restraints weight = 9172.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.073822 restraints weight = 8374.776| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 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 = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13660 Z= 0.158 Angle : 0.557 11.527 19702 Z= 0.328 Chirality : 0.033 0.174 2240 Planarity : 0.004 0.036 1477 Dihedral : 29.644 150.119 4170 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.51 % Favored : 97.25 % Rotamer: Outliers : 1.25 % Allowed : 17.20 % Favored : 81.55 % 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 aren not related in a simple way. whole: 2.64 (0.30), residues: 839 helix: 2.88 (0.22), residues: 562 sheet: 0.54 (1.20), residues: 20 loop : -0.86 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.021 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 covalent geometry : bond 0.00345 (13658) covalent geometry : angle 0.55747 (19696) hydrogen bonds : bond 0.04212 ( 773) hydrogen bonds : angle 2.78048 ( 1929) link_TRANS : bond 0.00048 ( 2) link_TRANS : angle 0.20034 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2236.61 seconds wall clock time: 39 minutes 7.35 seconds (2347.35 seconds total)