Starting phenix.real_space_refine on Wed Jul 30 16:49:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8txw_41707/07_2025/8txw_41707.cif Found real_map, /net/cci-nas-00/data/ceres_data/8txw_41707/07_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_41707/07_2025/8txw_41707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8txw_41707/07_2025/8txw_41707.map" model { file = "/net/cci-nas-00/data/ceres_data/8txw_41707/07_2025/8txw_41707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8txw_41707/07_2025/8txw_41707.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.54, per 1000 atoms: 0.67 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: 3.36 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 5.76 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: 4.54 Time building geometry restraints manager: 3.93 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 36.420 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.560 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.005 0.001 HIS H 82 PHE 0.007 0.001 PHE A 67 TYR 0.052 0.002 TYR F 88 ARG 0.008 0.000 ARG B 23 Details of bonding type rmsd link_TRANS : bond 0.00160 ( 2) link_TRANS : angle 0.39496 ( 6) hydrogen bonds : bond 0.11703 ( 773) hydrogen bonds : angle 3.88105 ( 1929) covalent geometry : bond 0.00359 (13658) covalent geometry : angle 0.54158 (19696) *********************** 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 : 1.121 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: 0.8248 (tm-30) REVERT: E 123 ASP cc_start: 0.9098 (m-30) cc_final: 0.8838 (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: 0.8565 (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: 0.8814 (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: 0.8415 (tm-30) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3531 time to fit residues: 82.8542 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 : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.103093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.066174 restraints weight = 44017.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.068800 restraints weight = 19073.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.070403 restraints weight = 12215.736| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13660 Z= 0.227 Angle : 0.584 8.039 19702 Z= 0.347 Chirality : 0.035 0.187 2240 Planarity : 0.004 0.036 1477 Dihedral : 29.746 150.339 4170 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.97 % Allowed : 9.15 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.30), residues: 839 helix: 2.80 (0.22), residues: 560 sheet: 0.33 (1.18), residues: 20 loop : -0.64 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.002 PHE A 67 TYR 0.044 0.002 TYR F 88 ARG 0.006 0.000 ARG F 23 Details of bonding type rmsd link_TRANS : bond 0.00054 ( 2) link_TRANS : angle 0.41064 ( 6) hydrogen bonds : bond 0.05159 ( 773) hydrogen bonds : angle 3.27931 ( 1929) covalent geometry : bond 0.00518 (13658) covalent geometry : angle 0.58398 (19696) *********************** 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 172 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 166 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 110 CYS cc_start: 0.8355 (t) cc_final: 0.7718 (t) REVERT: A 123 ASP cc_start: 0.9059 (m-30) cc_final: 0.8448 (m-30) REVERT: B 88 TYR cc_start: 0.8725 (m-10) cc_final: 0.8359 (m-10) REVERT: D 71 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8172 (tm-30) REVERT: E 122 LYS cc_start: 0.8918 (ptpp) cc_final: 0.8698 (ptpp) REVERT: E 129 ARG cc_start: 0.8592 (tpt90) cc_final: 0.8220 (tpt90) REVERT: G 64 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8826 (tm-30) outliers start: 6 outliers final: 6 residues processed: 168 average time/residue: 0.3434 time to fit residues: 76.3804 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 : 1.108 ------------------------------------------------------------------------------- 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 85 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 88 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.104170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.067278 restraints weight = 43989.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.069835 restraints weight = 18997.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.071638 restraints weight = 12214.863| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13660 Z= 0.175 Angle : 0.548 8.091 19702 Z= 0.327 Chirality : 0.033 0.189 2240 Planarity : 0.004 0.034 1477 Dihedral : 29.623 149.565 4170 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.11 % Allowed : 13.59 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.30), residues: 839 helix: 2.84 (0.22), residues: 561 sheet: 0.31 (1.19), residues: 20 loop : -0.74 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE A 67 TYR 0.031 0.002 TYR F 88 ARG 0.007 0.000 ARG F 23 Details of bonding type rmsd link_TRANS : bond 0.00041 ( 2) link_TRANS : angle 0.43476 ( 6) hydrogen bonds : bond 0.04553 ( 773) hydrogen bonds : angle 3.01763 ( 1929) covalent geometry : bond 0.00389 (13658) covalent geometry : angle 0.54786 (19696) *********************** 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 166 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8672 (pm20) cc_final: 0.8370 (pm20) REVERT: A 76 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8522 (tm-30) REVERT: A 110 CYS cc_start: 0.8390 (t) cc_final: 0.7770 (t) REVERT: A 123 ASP cc_start: 0.9106 (m-30) cc_final: 0.8346 (m-30) REVERT: B 88 TYR cc_start: 0.8508 (m-10) cc_final: 0.8224 (m-80) REVERT: E 123 ASP cc_start: 0.8718 (m-30) cc_final: 0.8446 (m-30) REVERT: E 129 ARG cc_start: 0.8580 (tpt90) cc_final: 0.8192 (tpt90) REVERT: G 64 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8711 (tm-30) outliers start: 7 outliers final: 6 residues processed: 161 average time/residue: 0.4313 time to fit residues: 93.7480 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 : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 49 optimal weight: 0.0980 chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 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 68 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.104812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.068916 restraints weight = 31579.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.071148 restraints weight = 15872.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.072611 restraints weight = 11061.041| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1354 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= 0.157 Angle : 0.539 8.575 19702 Z= 0.322 Chirality : 0.033 0.192 2240 Planarity : 0.004 0.034 1477 Dihedral : 29.579 149.759 4170 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.66 % Allowed : 14.70 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.30), residues: 839 helix: 2.89 (0.22), residues: 561 sheet: 0.49 (1.20), residues: 20 loop : -0.72 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.007 0.001 PHE E 67 TYR 0.025 0.001 TYR F 88 ARG 0.005 0.000 ARG D 86 Details of bonding type rmsd link_TRANS : bond 0.00080 ( 2) link_TRANS : angle 0.21469 ( 6) hydrogen bonds : bond 0.04280 ( 773) hydrogen bonds : angle 2.88249 ( 1929) covalent geometry : bond 0.00339 (13658) covalent geometry : angle 0.53943 (19696) *********************** 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 167 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8674 (pm20) cc_final: 0.8285 (pm20) REVERT: A 76 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8482 (tm-30) REVERT: B 88 TYR cc_start: 0.8545 (m-10) cc_final: 0.8137 (m-10) REVERT: E 129 ARG cc_start: 0.8543 (tpt90) cc_final: 0.8187 (tpt90) REVERT: F 25 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.8828 (t0) REVERT: G 64 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8431 (tt0) outliers start: 11 outliers final: 7 residues processed: 162 average time/residue: 0.4154 time to fit residues: 90.8581 Evaluate side-chains 157 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 0.0070 chunk 93 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.105142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.070149 restraints weight = 54863.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.072994 restraints weight = 21506.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.074116 restraints weight = 11648.012| |-----------------------------------------------------------------------------| 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 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1416 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= 0.153 Angle : 0.533 8.755 19702 Z= 0.319 Chirality : 0.033 0.177 2240 Planarity : 0.004 0.035 1477 Dihedral : 29.567 149.872 4170 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.03 % Favored : 97.85 % Rotamer: Outliers : 1.94 % Allowed : 15.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.30), residues: 839 helix: 2.92 (0.22), residues: 562 sheet: 0.63 (1.22), residues: 20 loop : -0.73 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.006 0.001 PHE A 67 TYR 0.020 0.001 TYR F 88 ARG 0.005 0.000 ARG D 86 Details of bonding type rmsd link_TRANS : bond 0.00029 ( 2) link_TRANS : angle 0.25626 ( 6) hydrogen bonds : bond 0.04201 ( 773) hydrogen bonds : angle 2.84126 ( 1929) covalent geometry : bond 0.00331 (13658) covalent geometry : angle 0.53304 (19696) *********************** 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 170 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8703 (pm20) cc_final: 0.8297 (pm20) REVERT: A 73 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6873 (mt-10) REVERT: A 76 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8472 (tm-30) REVERT: B 88 TYR cc_start: 0.8615 (m-10) cc_final: 0.8245 (m-10) REVERT: E 129 ARG cc_start: 0.8547 (tpt90) cc_final: 0.8189 (tpt90) REVERT: G 64 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8448 (tt0) outliers start: 13 outliers final: 9 residues processed: 162 average time/residue: 0.4094 time to fit residues: 91.1787 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 : 1.328 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 56 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 107 optimal weight: 0.4980 chunk 80 optimal weight: 0.0670 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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** 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 = 0.3584 r_free = 0.3584 target = 0.105386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.070228 restraints weight = 39293.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.072839 restraints weight = 17345.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.074395 restraints weight = 11209.591| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 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 = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13660 Z= 0.147 Angle : 0.528 8.796 19702 Z= 0.316 Chirality : 0.033 0.182 2240 Planarity : 0.004 0.035 1477 Dihedral : 29.541 149.950 4170 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.03 % Favored : 97.85 % Rotamer: Outliers : 2.08 % Allowed : 15.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.29), residues: 839 helix: 2.94 (0.22), residues: 562 sheet: 0.73 (1.24), residues: 20 loop : -0.71 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 113 PHE 0.008 0.001 PHE D 70 TYR 0.020 0.001 TYR C 39 ARG 0.007 0.000 ARG F 23 Details of bonding type rmsd link_TRANS : bond 0.00056 ( 2) link_TRANS : angle 0.22257 ( 6) hydrogen bonds : bond 0.04047 ( 773) hydrogen bonds : angle 2.77108 ( 1929) covalent geometry : bond 0.00315 (13658) covalent geometry : angle 0.52805 (19696) *********************** 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 169 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8698 (pm20) cc_final: 0.8253 (pm20) REVERT: A 73 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7167 (mt-10) REVERT: A 76 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8533 (tm-30) REVERT: B 88 TYR cc_start: 0.8757 (m-10) cc_final: 0.8297 (m-10) REVERT: E 129 ARG cc_start: 0.8555 (tpt90) cc_final: 0.8194 (tpt90) REVERT: F 25 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8319 (m110) REVERT: F 62 LEU cc_start: 0.9385 (mt) cc_final: 0.9042 (mt) REVERT: G 64 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8677 (tm-30) outliers start: 14 outliers final: 9 residues processed: 162 average time/residue: 0.2991 time to fit residues: 66.5880 Evaluate side-chains 160 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 112 ILE 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 47 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.104750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.067880 restraints weight = 43534.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.070508 restraints weight = 18907.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.072093 restraints weight = 12129.713| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 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 = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13660 Z= 0.179 Angle : 0.550 9.843 19702 Z= 0.325 Chirality : 0.033 0.187 2240 Planarity : 0.004 0.034 1477 Dihedral : 29.606 150.571 4170 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.15 % Favored : 97.73 % Rotamer: Outliers : 1.80 % Allowed : 16.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.30), residues: 839 helix: 2.94 (0.22), residues: 562 sheet: 0.69 (1.24), residues: 20 loop : -0.76 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.007 0.001 PHE A 67 TYR 0.021 0.001 TYR F 88 ARG 0.006 0.000 ARG D 86 Details of bonding type rmsd link_TRANS : bond 0.00020 ( 2) link_TRANS : angle 0.26579 ( 6) hydrogen bonds : bond 0.04353 ( 773) hydrogen bonds : angle 2.85410 ( 1929) covalent geometry : bond 0.00401 (13658) covalent geometry : angle 0.54990 (19696) *********************** 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 165 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8698 (pm20) cc_final: 0.8258 (pm20) REVERT: A 73 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7032 (mt-10) REVERT: A 76 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8524 (tm-30) REVERT: A 110 CYS cc_start: 0.8433 (t) cc_final: 0.8043 (t) REVERT: A 123 ASP cc_start: 0.9033 (m-30) cc_final: 0.8297 (m-30) REVERT: B 88 TYR cc_start: 0.8849 (m-10) cc_final: 0.8353 (m-80) REVERT: E 129 ARG cc_start: 0.8556 (tpt90) cc_final: 0.8204 (tpt90) REVERT: C 63 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9314 (mt) outliers start: 12 outliers final: 10 residues processed: 158 average time/residue: 0.3135 time to fit residues: 66.9793 Evaluate side-chains 164 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 63 LEU 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 38 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 40 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 105 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.105619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.068739 restraints weight = 46222.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.071349 restraints weight = 19331.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.073209 restraints weight = 12178.766| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 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 = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1644 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= 0.150 Angle : 0.541 10.728 19702 Z= 0.320 Chirality : 0.032 0.185 2240 Planarity : 0.004 0.035 1477 Dihedral : 29.581 150.230 4170 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.27 % Favored : 97.61 % Rotamer: Outliers : 1.53 % Allowed : 16.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.30), residues: 839 helix: 2.99 (0.22), residues: 562 sheet: 0.77 (1.25), residues: 20 loop : -0.77 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 75 PHE 0.006 0.001 PHE E 67 TYR 0.020 0.001 TYR C 39 ARG 0.007 0.000 ARG D 86 Details of bonding type rmsd link_TRANS : bond 0.00043 ( 2) link_TRANS : angle 0.21839 ( 6) hydrogen bonds : bond 0.04087 ( 773) hydrogen bonds : angle 2.75995 ( 1929) covalent geometry : bond 0.00325 (13658) covalent geometry : angle 0.54147 (19696) *********************** 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 162 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8658 (pm20) cc_final: 0.8265 (pm20) REVERT: A 73 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7121 (mt-10) REVERT: A 76 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8528 (tm-30) REVERT: A 110 CYS cc_start: 0.8437 (t) cc_final: 0.7984 (t) REVERT: A 123 ASP cc_start: 0.8975 (m-30) cc_final: 0.8186 (m-30) REVERT: B 88 TYR cc_start: 0.8857 (m-10) cc_final: 0.8395 (m-80) REVERT: E 129 ARG cc_start: 0.8547 (tpt90) cc_final: 0.8202 (tpt90) REVERT: F 25 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8635 (t0) REVERT: C 63 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9296 (mt) REVERT: G 64 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8828 (tm-30) outliers start: 10 outliers final: 7 residues processed: 158 average time/residue: 0.2932 time to fit residues: 62.9455 Evaluate side-chains 158 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain C residue 63 LEU 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 107 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 ** 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 = 0.3532 r_free = 0.3532 target = 0.102526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.067089 restraints weight = 33315.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.069355 restraints weight = 17103.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.070659 restraints weight = 11955.659| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13660 Z= 0.230 Angle : 0.597 11.741 19702 Z= 0.349 Chirality : 0.035 0.174 2240 Planarity : 0.004 0.035 1477 Dihedral : 29.813 151.174 4170 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.75 % Favored : 97.13 % Rotamer: Outliers : 1.80 % Allowed : 16.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.30), residues: 839 helix: 2.87 (0.22), residues: 560 sheet: 0.52 (1.24), residues: 20 loop : -0.90 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.002 PHE B 61 TYR 0.032 0.002 TYR F 88 ARG 0.006 0.000 ARG D 86 Details of bonding type rmsd link_TRANS : bond 0.00072 ( 2) link_TRANS : angle 0.37332 ( 6) hydrogen bonds : bond 0.05080 ( 773) hydrogen bonds : angle 3.06084 ( 1929) covalent geometry : bond 0.00529 (13658) covalent geometry : angle 0.59740 (19696) *********************** 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 164 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8655 (pm20) cc_final: 0.8263 (pm20) REVERT: A 73 GLU cc_start: 0.7497 (mt-10) cc_final: 0.6330 (mt-10) REVERT: A 76 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8601 (tm-30) REVERT: A 123 ASP cc_start: 0.9044 (m-30) cc_final: 0.8801 (m-30) REVERT: B 88 TYR cc_start: 0.8937 (m-10) cc_final: 0.8408 (m-80) REVERT: E 129 ARG cc_start: 0.8550 (tpt90) cc_final: 0.8184 (tpt90) REVERT: F 25 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8749 (t0) REVERT: H 93 GLU cc_start: 0.8031 (pm20) cc_final: 0.7667 (pt0) REVERT: G 64 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8848 (tm-30) outliers start: 12 outliers final: 8 residues processed: 159 average time/residue: 0.3074 time to fit residues: 65.6764 Evaluate side-chains 160 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 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 15 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 67 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.104608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.068711 restraints weight = 49934.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.071412 restraints weight = 19612.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.073304 restraints weight = 12037.511| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 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 = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1783 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= 0.154 Angle : 0.552 11.098 19702 Z= 0.325 Chirality : 0.033 0.207 2240 Planarity : 0.004 0.035 1477 Dihedral : 29.641 149.872 4170 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.63 % Favored : 97.25 % Rotamer: Outliers : 1.39 % Allowed : 16.78 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.30), residues: 839 helix: 2.96 (0.22), residues: 561 sheet: 0.65 (1.26), residues: 20 loop : -0.92 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE E 67 TYR 0.020 0.001 TYR C 39 ARG 0.007 0.000 ARG D 86 Details of bonding type rmsd link_TRANS : bond 0.00052 ( 2) link_TRANS : angle 0.26391 ( 6) hydrogen bonds : bond 0.04192 ( 773) hydrogen bonds : angle 2.79156 ( 1929) covalent geometry : bond 0.00333 (13658) covalent geometry : angle 0.55247 (19696) ********************** 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 160 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8669 (pm20) cc_final: 0.8234 (pm20) REVERT: A 76 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8433 (tm-30) REVERT: A 110 CYS cc_start: 0.8480 (t) cc_final: 0.7807 (t) REVERT: A 123 ASP cc_start: 0.8976 (m-30) cc_final: 0.8267 (m-30) REVERT: B 88 TYR cc_start: 0.8891 (m-10) cc_final: 0.8412 (m-80) REVERT: E 129 ARG cc_start: 0.8562 (tpt90) cc_final: 0.8201 (tpt90) REVERT: F 25 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8561 (t0) REVERT: G 64 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8837 (tm-30) outliers start: 9 outliers final: 7 residues processed: 157 average time/residue: 0.3176 time to fit residues: 67.2631 Evaluate side-chains 156 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 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 15 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 82 optimal weight: 8.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 ** 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 = 0.3581 r_free = 0.3581 target = 0.105166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.067657 restraints weight = 55136.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.070452 restraints weight = 21394.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.072376 restraints weight = 12928.702| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 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 = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1791 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= 0.158 Angle : 0.558 11.705 19702 Z= 0.328 Chirality : 0.033 0.181 2240 Planarity : 0.004 0.035 1477 Dihedral : 29.633 150.159 4170 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.30), residues: 839 helix: 2.92 (0.22), residues: 561 sheet: 0.63 (1.25), residues: 20 loop : -0.92 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.006 0.001 PHE E 67 TYR 0.021 0.002 TYR C 39 ARG 0.007 0.000 ARG D 86 Details of bonding type rmsd link_TRANS : bond 0.00040 ( 2) link_TRANS : angle 0.20611 ( 6) hydrogen bonds : bond 0.04196 ( 773) hydrogen bonds : angle 2.79693 ( 1929) covalent geometry : bond 0.00348 (13658) covalent geometry : angle 0.55769 (19696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4824.54 seconds wall clock time: 87 minutes 8.21 seconds (5228.21 seconds total)