Starting phenix.real_space_refine on Sat Aug 23 11:18:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eue_28612/08_2025/8eue_28612_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eue_28612/08_2025/8eue_28612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eue_28612/08_2025/8eue_28612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eue_28612/08_2025/8eue_28612.map" model { file = "/net/cci-nas-00/data/ceres_data/8eue_28612/08_2025/8eue_28612_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eue_28612/08_2025/8eue_28612_neut.cif" } resolution = 3.48 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= 0.004 sd= 0.104 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 292 5.49 5 S 12 5.16 5 C 6592 2.51 5 N 2216 2.21 5 O 2814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 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: 11926 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 780 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 616 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 704 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3011 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3010 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 798 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU B 22 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU B 22 " occ=0.00 residue: pdb=" N ARG B 23 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG B 23 " occ=0.00 Time building chain proxies: 2.56, per 1000 atoms: 0.21 Number of scatterers: 11926 At special positions: 0 Unit cell: (116.9, 121.075, 105.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 292 15.00 O 2814 8.00 N 2216 7.00 C 6592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 295.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 73.0% alpha, 1.9% beta 146 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.659A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.547A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.768A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.693A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.646A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.374A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 4.094A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.899A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.766A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 4.102A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.892A pdb=" N LEU D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 4.126A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.530A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.649A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.348A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 4.206A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.645A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.778A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 99 removed outlier: 3.595A pdb=" N LEU H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 45 through 72 removed outlier: 4.131A pdb=" N VAL K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 89 removed outlier: 3.626A pdb=" N LEU K 83 " --> pdb=" O ILE K 79 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN K 89 " --> pdb=" O LEU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 97 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.522A 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: 6.778A pdb=" N THR B 96 " --> pdb=" O THR K 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.084A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'H' and resid 85 through 86 385 hydrogen bonds defined for protein. 1140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 352 hydrogen bonds 704 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1765 1.33 - 1.45: 4768 1.45 - 1.58: 5595 1.58 - 1.70: 585 1.70 - 1.83: 22 Bond restraints: 12735 Sorted by residual: bond pdb=" CG1 ILE H 58 " pdb=" CD1 ILE H 58 " ideal model delta sigma weight residual 1.513 1.403 0.110 3.90e-02 6.57e+02 7.94e+00 bond pdb=" C ILE C 79 " pdb=" N PRO C 80 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.08e-02 8.57e+03 5.77e+00 bond pdb=" CB ILE E 51 " pdb=" CG2 ILE E 51 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.95e+00 bond pdb=" CB PHE H 67 " pdb=" CG PHE H 67 " ideal model delta sigma weight residual 1.502 1.553 -0.051 2.30e-02 1.89e+03 4.93e+00 bond pdb=" CG LEU F 62 " pdb=" CD1 LEU F 62 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.91e+00 ... (remaining 12730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.03: 18412 8.03 - 16.06: 47 16.06 - 24.09: 5 24.09 - 32.12: 2 32.12 - 40.15: 2 Bond angle restraints: 18468 Sorted by residual: angle pdb=" OP1 DG I -43 " pdb=" P DG I -43 " pdb=" OP2 DG I -43 " ideal model delta sigma weight residual 120.00 79.85 40.15 3.00e+00 1.11e-01 1.79e+02 angle pdb=" OP2 DG I -43 " pdb=" P DG I -43 " pdb=" O5' DG I -43 " ideal model delta sigma weight residual 108.00 69.44 38.56 3.00e+00 1.11e-01 1.65e+02 angle pdb=" OP1 DG I -43 " pdb=" P DG I -43 " pdb=" O5' DG I -43 " ideal model delta sigma weight residual 109.00 137.36 -28.36 3.00e+00 1.11e-01 8.93e+01 angle pdb=" O3' DA I -44 " pdb=" P DG I -43 " pdb=" OP2 DG I -43 " ideal model delta sigma weight residual 108.00 133.18 -25.18 3.00e+00 1.11e-01 7.04e+01 angle pdb=" O3' DA I -44 " pdb=" P DG I -43 " pdb=" OP1 DG I -43 " ideal model delta sigma weight residual 108.00 84.68 23.32 3.00e+00 1.11e-01 6.04e+01 ... (remaining 18463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.47: 4035 18.47 - 36.95: 1286 36.95 - 55.42: 1339 55.42 - 73.90: 284 73.90 - 92.37: 46 Dihedral angle restraints: 6990 sinusoidal: 4813 harmonic: 2177 Sorted by residual: dihedral pdb=" CA ILE F 50 " pdb=" C ILE F 50 " pdb=" N TYR F 51 " pdb=" CA TYR F 51 " ideal model delta harmonic sigma weight residual 180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ARG A 63 " pdb=" C ARG A 63 " pdb=" N LYS A 64 " pdb=" CA LYS A 64 " ideal model delta harmonic sigma weight residual -180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual -180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 6987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 2028 0.141 - 0.282: 71 0.282 - 0.423: 5 0.423 - 0.564: 0 0.564 - 0.705: 1 Chirality restraints: 2105 Sorted by residual: chirality pdb=" P DG I -43 " pdb=" OP1 DG I -43 " pdb=" OP2 DG I -43 " pdb=" O5' DG I -43 " both_signs ideal model delta sigma weight residual True 2.35 1.64 0.71 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CB VAL B 70 " pdb=" CA VAL B 70 " pdb=" CG1 VAL B 70 " pdb=" CG2 VAL B 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 2102 not shown) Planarity restraints: 1325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 80 " 0.016 2.00e-02 2.50e+03 3.57e-02 2.55e+01 pdb=" CG TYR D 80 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TYR D 80 " 0.051 2.00e-02 2.50e+03 pdb=" CD2 TYR D 80 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR D 80 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR D 80 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR D 80 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 80 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 120 " 0.063 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO A 121 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " -0.062 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO A 43 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.050 5.00e-02 4.00e+02 ... (remaining 1322 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2143 2.77 - 3.31: 10534 3.31 - 3.84: 25256 3.84 - 4.37: 27544 4.37 - 4.90: 38028 Nonbonded interactions: 103505 Sorted by model distance: nonbonded pdb=" OG SER H 75 " pdb=" O TYR K 39 " model vdw 2.242 3.040 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.244 3.040 nonbonded pdb=" O ARG H 76 " pdb=" NH1 ARG H 76 " model vdw 2.250 3.120 nonbonded pdb=" O LYS D 54 " pdb=" OG SER D 57 " model vdw 2.266 3.040 nonbonded pdb=" O LEU A 92 " pdb=" OG SER A 96 " model vdw 2.271 3.040 ... (remaining 103500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 41 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 84 or (resid 85 and (name N or nam \ e CA or name C or name O or name CB )) or resid 86 through 129 or (resid 130 and \ (name N or name CA or name C or name O or name CB )) or resid 131 through 135)) \ selection = (chain 'E' and resid 41 through 135) } ncs_group { reference = (chain 'B' and resid 24 through 102) selection = (chain 'F' and (resid 24 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 or (resid 46 and (name N or name CA or nam \ e C or name O or name CB )) or resid 47 through 49 or (resid 50 through 51 and ( \ name N or name CA or name C or name O or name CB )) or resid 52 through 61 or (r \ esid 62 and (name N or name CA or name C or name O or name CB )) or resid 63 thr \ ough 65 or (resid 66 and (name N or name CA or name C or name O or name CB )) or \ resid 67 through 87 or (resid 88 through 89 and (name N or name CA or name C or \ name O or name CB )) or resid 90 through 102)) } ncs_group { reference = (chain 'C' and (resid 15 through 50 or (resid 51 through 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 114 or (resid 115 and ( \ name N or name CA or name C or name O or name CB )) or resid 116 through 118)) selection = chain 'K' } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 31 through 53 or (resid 54 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 121)) } ncs_group { reference = (chain 'I' and (resid -73 through -1 or resid 1 through 73)) selection = (chain 'J' and (resid -73 through -1 or resid 1 through 73)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.340 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.060 Find NCS groups from input model: 0.170 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.007 0.110 12735 Z= 0.297 Angle : 1.331 40.147 18468 Z= 0.678 Chirality : 0.061 0.705 2105 Planarity : 0.011 0.110 1325 Dihedral : 31.225 92.370 5584 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 41.83 % Favored : 58.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.26), residues: 735 helix: -1.43 (0.19), residues: 504 sheet: None (None), residues: 0 loop : -1.74 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG H 76 TYR 0.080 0.005 TYR D 80 PHE 0.018 0.002 PHE H 62 HIS 0.010 0.002 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00675 (12735) covalent geometry : angle 1.33127 (18468) hydrogen bonds : bond 0.10831 ( 737) hydrogen bonds : angle 5.18973 ( 1844) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7633 (t0) cc_final: 0.6992 (m-30) REVERT: A 131 ARG cc_start: 0.7638 (mmt180) cc_final: 0.7438 (mmt180) REVERT: D 90 GLU cc_start: 0.8585 (mp0) cc_final: 0.8339 (mp0) REVERT: E 76 GLN cc_start: 0.8387 (pp30) cc_final: 0.8081 (pp30) REVERT: E 90 MET cc_start: 0.8511 (mpp) cc_final: 0.8286 (mpp) REVERT: H 60 ASN cc_start: 0.9153 (t0) cc_final: 0.8756 (t0) REVERT: H 64 ASN cc_start: 0.8489 (m-40) cc_final: 0.8069 (m110) REVERT: H 92 GLN cc_start: 0.8272 (pp30) cc_final: 0.7596 (pp30) REVERT: H 102 GLU cc_start: 0.8063 (pm20) cc_final: 0.7683 (mp0) REVERT: H 103 LEU cc_start: 0.8908 (tp) cc_final: 0.7803 (tp) REVERT: K 75 LYS cc_start: 0.8489 (tppt) cc_final: 0.8129 (tppp) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.1168 time to fit residues: 44.8017 Evaluate side-chains 260 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 ASN K 89 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.078919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.063520 restraints weight = 52990.917| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.13 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12735 Z= 0.182 Angle : 0.882 38.893 18468 Z= 0.447 Chirality : 0.039 0.440 2105 Planarity : 0.006 0.080 1325 Dihedral : 32.911 94.419 4133 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.72 % Allowed : 34.97 % Favored : 59.31 % 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: -0.56 (0.29), residues: 735 helix: 0.16 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -1.49 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 76 TYR 0.025 0.002 TYR F 88 PHE 0.020 0.002 PHE H 67 HIS 0.008 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00399 (12735) covalent geometry : angle 0.88245 (18468) hydrogen bonds : bond 0.05050 ( 737) hydrogen bonds : angle 3.76029 ( 1844) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 266 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8659 (t0) cc_final: 0.8363 (t0) REVERT: D 57 SER cc_start: 0.9388 (m) cc_final: 0.9172 (p) REVERT: D 90 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8301 (mp0) REVERT: E 73 GLU cc_start: 0.7680 (mm-30) cc_final: 0.6825 (mm-30) REVERT: E 76 GLN cc_start: 0.8289 (pp30) cc_final: 0.7680 (pp30) REVERT: F 85 ASP cc_start: 0.8338 (p0) cc_final: 0.8127 (p0) REVERT: H 60 ASN cc_start: 0.9203 (t0) cc_final: 0.8698 (t0) REVERT: H 64 ASN cc_start: 0.8804 (m-40) cc_final: 0.8283 (m110) REVERT: H 73 GLU cc_start: 0.8651 (tp30) cc_final: 0.8357 (tp30) REVERT: H 92 GLN cc_start: 0.8122 (pp30) cc_final: 0.7519 (pp30) REVERT: K 35 ARG cc_start: 0.8845 (mtt-85) cc_final: 0.8545 (mmm-85) REVERT: K 90 ASP cc_start: 0.8312 (t0) cc_final: 0.7951 (t70) outliers start: 35 outliers final: 22 residues processed: 280 average time/residue: 0.1175 time to fit residues: 45.0018 Evaluate side-chains 267 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 244 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 98 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN K 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.079770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.064211 restraints weight = 53041.675| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.16 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12735 Z= 0.173 Angle : 0.868 39.437 18468 Z= 0.436 Chirality : 0.039 0.448 2105 Planarity : 0.005 0.075 1325 Dihedral : 32.628 91.506 4133 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.72 % Allowed : 34.80 % Favored : 59.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.30), residues: 735 helix: 0.79 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.27 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 78 TYR 0.025 0.002 TYR F 88 PHE 0.021 0.002 PHE H 67 HIS 0.008 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00380 (12735) covalent geometry : angle 0.86795 (18468) hydrogen bonds : bond 0.04635 ( 737) hydrogen bonds : angle 3.59419 ( 1844) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 274 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8855 (t0) cc_final: 0.8598 (t0) REVERT: A 129 ARG cc_start: 0.8714 (tpt90) cc_final: 0.8265 (tpt90) REVERT: C 116 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8521 (pp) REVERT: D 56 MET cc_start: 0.9147 (tpt) cc_final: 0.8854 (tpt) REVERT: D 57 SER cc_start: 0.9430 (m) cc_final: 0.9196 (p) REVERT: D 83 ARG cc_start: 0.8017 (mmp80) cc_final: 0.7761 (mmp80) REVERT: E 73 GLU cc_start: 0.7718 (mm-30) cc_final: 0.6814 (mm-30) REVERT: E 76 GLN cc_start: 0.8275 (pp30) cc_final: 0.7602 (pp30) REVERT: E 105 GLU cc_start: 0.8375 (tt0) cc_final: 0.7801 (tm-30) REVERT: F 40 ARG cc_start: 0.9007 (ttm170) cc_final: 0.8774 (ttt180) REVERT: F 51 TYR cc_start: 0.7829 (m-80) cc_final: 0.7618 (m-80) REVERT: H 60 ASN cc_start: 0.9180 (t0) cc_final: 0.8742 (t0) REVERT: H 64 ASN cc_start: 0.8867 (m-40) cc_final: 0.8364 (m-40) REVERT: H 76 ARG cc_start: 0.8784 (tpt90) cc_final: 0.8479 (tpt90) REVERT: H 80 TYR cc_start: 0.7270 (t80) cc_final: 0.6918 (t80) REVERT: H 84 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.7953 (p) REVERT: H 92 GLN cc_start: 0.8209 (pp30) cc_final: 0.7570 (pp30) REVERT: K 29 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8098 (ttp80) outliers start: 35 outliers final: 22 residues processed: 288 average time/residue: 0.1294 time to fit residues: 50.1893 Evaluate side-chains 273 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 85 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 98 optimal weight: 0.0270 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.080346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.064716 restraints weight = 53127.869| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.13 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12735 Z= 0.168 Angle : 0.866 39.475 18468 Z= 0.433 Chirality : 0.039 0.437 2105 Planarity : 0.005 0.072 1325 Dihedral : 32.483 89.760 4133 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 6.37 % Allowed : 36.60 % Favored : 57.03 % 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: 0.64 (0.31), residues: 735 helix: 1.06 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.03 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 78 TYR 0.030 0.002 TYR F 88 PHE 0.022 0.001 PHE H 67 HIS 0.008 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00365 (12735) covalent geometry : angle 0.86597 (18468) hydrogen bonds : bond 0.04454 ( 737) hydrogen bonds : angle 3.52286 ( 1844) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 275 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8781 (mm-30) REVERT: A 106 ASP cc_start: 0.8785 (t0) cc_final: 0.8231 (t0) REVERT: A 129 ARG cc_start: 0.8679 (tpt90) cc_final: 0.8350 (tpt90) REVERT: C 64 GLU cc_start: 0.8882 (tp30) cc_final: 0.8643 (tp30) REVERT: D 57 SER cc_start: 0.9386 (m) cc_final: 0.9132 (p) REVERT: D 90 GLU cc_start: 0.8594 (mp0) cc_final: 0.7788 (mp0) REVERT: E 73 GLU cc_start: 0.7760 (mm-30) cc_final: 0.6806 (mm-30) REVERT: E 76 GLN cc_start: 0.8246 (pp30) cc_final: 0.7594 (pp30) REVERT: E 105 GLU cc_start: 0.8372 (tt0) cc_final: 0.7783 (tm-30) REVERT: F 39 ARG cc_start: 0.8581 (tpp-160) cc_final: 0.8082 (mmt-90) REVERT: F 40 ARG cc_start: 0.9025 (ttm170) cc_final: 0.8773 (ttt180) REVERT: F 50 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8011 (pt) REVERT: H 60 ASN cc_start: 0.9141 (t0) cc_final: 0.8705 (t0) REVERT: H 64 ASN cc_start: 0.8814 (m-40) cc_final: 0.8352 (m-40) REVERT: H 92 GLN cc_start: 0.8198 (pp30) cc_final: 0.7607 (pp30) REVERT: K 29 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8066 (ttp80) REVERT: K 75 LYS cc_start: 0.8997 (mmtp) cc_final: 0.8787 (mmtp) outliers start: 39 outliers final: 25 residues processed: 293 average time/residue: 0.1365 time to fit residues: 53.8260 Evaluate side-chains 279 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 252 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 113 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.080615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.064900 restraints weight = 53304.137| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.15 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12735 Z= 0.169 Angle : 0.873 39.510 18468 Z= 0.434 Chirality : 0.039 0.431 2105 Planarity : 0.005 0.073 1325 Dihedral : 32.411 89.122 4133 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 6.37 % Allowed : 37.58 % Favored : 56.05 % 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: 0.79 (0.31), residues: 735 helix: 1.17 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -0.97 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 78 TYR 0.024 0.002 TYR F 88 PHE 0.009 0.001 PHE E 104 HIS 0.009 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00368 (12735) covalent geometry : angle 0.87305 (18468) hydrogen bonds : bond 0.04477 ( 737) hydrogen bonds : angle 3.49869 ( 1844) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 270 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8689 (tp-100) REVERT: A 97 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8746 (mm-30) REVERT: C 64 GLU cc_start: 0.8981 (tp30) cc_final: 0.8648 (tp30) REVERT: D 57 SER cc_start: 0.9404 (m) cc_final: 0.9124 (p) REVERT: D 90 GLU cc_start: 0.8585 (mp0) cc_final: 0.7891 (mp0) REVERT: E 73 GLU cc_start: 0.7801 (mm-30) cc_final: 0.6860 (mm-30) REVERT: E 76 GLN cc_start: 0.8289 (pp30) cc_final: 0.7614 (pp30) REVERT: E 112 ILE cc_start: 0.9381 (mp) cc_final: 0.9171 (mp) REVERT: H 60 ASN cc_start: 0.9139 (t0) cc_final: 0.8682 (t0) REVERT: H 64 ASN cc_start: 0.8892 (m-40) cc_final: 0.8400 (m-40) REVERT: H 80 TYR cc_start: 0.7082 (t80) cc_final: 0.6534 (t80) REVERT: H 84 SER cc_start: 0.8329 (OUTLIER) cc_final: 0.7988 (p) REVERT: H 92 GLN cc_start: 0.8179 (pp30) cc_final: 0.7598 (pp30) REVERT: K 29 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8019 (ttp80) REVERT: K 75 LYS cc_start: 0.8994 (mmtp) cc_final: 0.8761 (mmtp) REVERT: K 90 ASP cc_start: 0.8355 (t0) cc_final: 0.7856 (t70) outliers start: 39 outliers final: 25 residues processed: 288 average time/residue: 0.1327 time to fit residues: 51.6305 Evaluate side-chains 272 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 245 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 113 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN D 79 HIS E 125 GLN F 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.073820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.058417 restraints weight = 54686.546| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.94 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 12735 Z= 0.298 Angle : 0.957 39.583 18468 Z= 0.491 Chirality : 0.044 0.401 2105 Planarity : 0.007 0.098 1325 Dihedral : 32.889 90.912 4133 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 7.19 % Allowed : 38.73 % Favored : 54.08 % 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: 0.24 (0.30), residues: 735 helix: 0.71 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.08 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 78 TYR 0.022 0.003 TYR F 88 PHE 0.020 0.002 PHE E 104 HIS 0.007 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00664 (12735) covalent geometry : angle 0.95679 (18468) hydrogen bonds : bond 0.06963 ( 737) hydrogen bonds : angle 4.01767 ( 1844) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 253 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9151 (tp-100) cc_final: 0.8867 (tm-30) REVERT: A 82 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8861 (tt) REVERT: B 39 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7197 (mpp-170) REVERT: C 64 GLU cc_start: 0.9114 (tp30) cc_final: 0.8730 (tp30) REVERT: D 57 SER cc_start: 0.9549 (m) cc_final: 0.9297 (p) REVERT: D 90 GLU cc_start: 0.8713 (mp0) cc_final: 0.8394 (mp0) REVERT: E 76 GLN cc_start: 0.8407 (pp30) cc_final: 0.7939 (pp30) REVERT: E 112 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9193 (mp) REVERT: E 133 GLU cc_start: 0.8172 (mp0) cc_final: 0.7610 (mp0) REVERT: E 134 ARG cc_start: 0.8605 (ttm170) cc_final: 0.8166 (tmm-80) REVERT: H 56 MET cc_start: 0.9129 (mmm) cc_final: 0.8873 (tpt) REVERT: H 60 ASN cc_start: 0.9280 (t0) cc_final: 0.8891 (t0) REVERT: H 64 ASN cc_start: 0.8958 (m-40) cc_final: 0.8658 (m-40) REVERT: H 73 GLU cc_start: 0.8772 (tp30) cc_final: 0.8557 (tp30) REVERT: H 92 GLN cc_start: 0.8321 (pp30) cc_final: 0.7632 (pp30) REVERT: K 29 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.7675 (ttp80) outliers start: 44 outliers final: 28 residues processed: 278 average time/residue: 0.1240 time to fit residues: 46.6031 Evaluate side-chains 270 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 113 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.078314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.062779 restraints weight = 53272.888| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.08 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12735 Z= 0.180 Angle : 0.913 39.489 18468 Z= 0.454 Chirality : 0.040 0.420 2105 Planarity : 0.005 0.074 1325 Dihedral : 32.564 89.117 4133 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.07 % Allowed : 39.54 % Favored : 55.39 % 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: 0.68 (0.31), residues: 735 helix: 1.08 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -0.98 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 78 TYR 0.032 0.002 TYR F 88 PHE 0.018 0.001 PHE A 67 HIS 0.009 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00399 (12735) covalent geometry : angle 0.91297 (18468) hydrogen bonds : bond 0.04762 ( 737) hydrogen bonds : angle 3.68384 ( 1844) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 266 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8682 (tp-100) REVERT: C 64 GLU cc_start: 0.8961 (tp30) cc_final: 0.8642 (tp30) REVERT: D 57 SER cc_start: 0.9452 (m) cc_final: 0.9185 (p) REVERT: D 90 GLU cc_start: 0.8658 (mp0) cc_final: 0.8177 (mp0) REVERT: E 76 GLN cc_start: 0.8353 (pp30) cc_final: 0.7885 (pp30) REVERT: E 112 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.9173 (mp) REVERT: E 133 GLU cc_start: 0.8042 (mp0) cc_final: 0.7255 (mp0) REVERT: E 134 ARG cc_start: 0.8415 (ttm170) cc_final: 0.8024 (tmm-80) REVERT: F 40 ARG cc_start: 0.9029 (ttm170) cc_final: 0.8794 (ttt180) REVERT: H 56 MET cc_start: 0.9099 (mmm) cc_final: 0.8890 (tpt) REVERT: H 60 ASN cc_start: 0.9168 (t0) cc_final: 0.8682 (t0) REVERT: H 64 ASN cc_start: 0.9000 (m-40) cc_final: 0.8340 (m-40) REVERT: H 73 GLU cc_start: 0.8657 (tp30) cc_final: 0.8369 (tp30) REVERT: H 92 GLN cc_start: 0.8262 (pp30) cc_final: 0.7623 (pp30) REVERT: K 29 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7688 (ttp80) REVERT: K 90 ASP cc_start: 0.8293 (t0) cc_final: 0.7727 (t70) outliers start: 31 outliers final: 22 residues processed: 284 average time/residue: 0.1262 time to fit residues: 48.6295 Evaluate side-chains 272 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 248 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 113 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 51 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 36 optimal weight: 0.0370 chunk 22 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.079634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.063927 restraints weight = 53006.148| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.08 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12735 Z= 0.174 Angle : 0.917 39.470 18468 Z= 0.452 Chirality : 0.041 0.430 2105 Planarity : 0.005 0.075 1325 Dihedral : 32.392 88.809 4133 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.07 % Allowed : 40.69 % Favored : 54.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.31), residues: 735 helix: 1.13 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -0.95 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 78 TYR 0.035 0.002 TYR F 88 PHE 0.019 0.001 PHE H 67 HIS 0.010 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00388 (12735) covalent geometry : angle 0.91683 (18468) hydrogen bonds : bond 0.04601 ( 737) hydrogen bonds : angle 3.69113 ( 1844) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 258 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8926 (tp30) cc_final: 0.8674 (tp30) REVERT: D 57 SER cc_start: 0.9419 (m) cc_final: 0.9154 (p) REVERT: D 90 GLU cc_start: 0.8642 (mp0) cc_final: 0.8229 (mp0) REVERT: E 59 GLU cc_start: 0.8798 (tp30) cc_final: 0.8456 (tp30) REVERT: E 76 GLN cc_start: 0.8354 (pp30) cc_final: 0.7861 (pp30) REVERT: E 112 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9179 (mp) REVERT: F 39 ARG cc_start: 0.8694 (tpp-160) cc_final: 0.8406 (tpp-160) REVERT: F 40 ARG cc_start: 0.8952 (ttm170) cc_final: 0.8697 (ttt180) REVERT: H 60 ASN cc_start: 0.9169 (t0) cc_final: 0.8640 (t0) REVERT: H 64 ASN cc_start: 0.8921 (m-40) cc_final: 0.8378 (m110) REVERT: H 73 GLU cc_start: 0.8640 (tp30) cc_final: 0.8408 (tp30) REVERT: H 89 ARG cc_start: 0.7594 (ptm160) cc_final: 0.7293 (ptm160) REVERT: H 92 GLN cc_start: 0.8174 (pp30) cc_final: 0.7570 (pp30) REVERT: K 29 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8005 (ttp80) REVERT: K 75 LYS cc_start: 0.8915 (mmtp) cc_final: 0.8686 (mmtp) outliers start: 31 outliers final: 23 residues processed: 276 average time/residue: 0.1240 time to fit residues: 46.5246 Evaluate side-chains 266 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 113 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 0.1980 chunk 87 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** 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 = 0.3841 r_free = 0.3841 target = 0.081023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.065495 restraints weight = 53246.953| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.06 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12735 Z= 0.172 Angle : 0.929 39.484 18468 Z= 0.457 Chirality : 0.040 0.429 2105 Planarity : 0.005 0.074 1325 Dihedral : 32.231 88.939 4133 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 5.07 % Allowed : 40.85 % Favored : 54.08 % 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: 0.78 (0.31), residues: 735 helix: 1.16 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -0.96 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 78 TYR 0.035 0.002 TYR F 88 PHE 0.009 0.001 PHE C 25 HIS 0.011 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00384 (12735) covalent geometry : angle 0.92946 (18468) hydrogen bonds : bond 0.04390 ( 737) hydrogen bonds : angle 3.70741 ( 1844) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 254 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8507 (tt) REVERT: A 97 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8833 (mm-30) REVERT: C 116 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8659 (pp) REVERT: D 57 SER cc_start: 0.9319 (m) cc_final: 0.9062 (p) REVERT: D 90 GLU cc_start: 0.8531 (mp0) cc_final: 0.8091 (mp0) REVERT: E 59 GLU cc_start: 0.8748 (tp30) cc_final: 0.8485 (tp30) REVERT: E 76 GLN cc_start: 0.8395 (pp30) cc_final: 0.7933 (pp30) REVERT: E 112 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9151 (mp) REVERT: F 39 ARG cc_start: 0.8688 (tpp-160) cc_final: 0.8421 (tpp-160) REVERT: H 60 ASN cc_start: 0.9101 (t0) cc_final: 0.8568 (t0) REVERT: H 64 ASN cc_start: 0.8828 (m-40) cc_final: 0.8305 (m110) REVERT: H 73 GLU cc_start: 0.8559 (tp30) cc_final: 0.8319 (tp30) REVERT: H 80 TYR cc_start: 0.7395 (t80) cc_final: 0.6878 (t80) REVERT: H 92 GLN cc_start: 0.8159 (pp30) cc_final: 0.7534 (pp30) REVERT: K 29 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8039 (ttp80) REVERT: K 75 LYS cc_start: 0.8887 (mmtp) cc_final: 0.8667 (mmtp) outliers start: 31 outliers final: 24 residues processed: 269 average time/residue: 0.1233 time to fit residues: 45.2598 Evaluate side-chains 270 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 242 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain K residue 113 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.080587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.064969 restraints weight = 53960.266| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.03 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12735 Z= 0.178 Angle : 0.943 39.488 18468 Z= 0.463 Chirality : 0.041 0.425 2105 Planarity : 0.005 0.078 1325 Dihedral : 32.218 88.753 4133 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.41 % Allowed : 42.16 % Favored : 53.43 % 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: 0.73 (0.31), residues: 735 helix: 1.14 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.10 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 78 TYR 0.033 0.002 TYR F 88 PHE 0.018 0.002 PHE H 67 HIS 0.011 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00396 (12735) covalent geometry : angle 0.94308 (18468) hydrogen bonds : bond 0.04522 ( 737) hydrogen bonds : angle 3.71832 ( 1844) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 245 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8482 (tt) REVERT: A 97 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8835 (mm-30) REVERT: C 116 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8682 (pp) REVERT: D 57 SER cc_start: 0.9340 (m) cc_final: 0.9074 (p) REVERT: D 90 GLU cc_start: 0.8551 (mp0) cc_final: 0.8086 (mp0) REVERT: E 59 GLU cc_start: 0.8824 (tp30) cc_final: 0.8539 (tp30) REVERT: E 76 GLN cc_start: 0.8404 (pp30) cc_final: 0.7938 (pp30) REVERT: E 112 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9167 (mp) REVERT: F 39 ARG cc_start: 0.8683 (tpp-160) cc_final: 0.8408 (tpp-160) REVERT: H 64 ASN cc_start: 0.8860 (m-40) cc_final: 0.8492 (m-40) REVERT: H 73 GLU cc_start: 0.8602 (tp30) cc_final: 0.8333 (tp30) REVERT: H 80 TYR cc_start: 0.7454 (t80) cc_final: 0.6932 (t80) REVERT: H 92 GLN cc_start: 0.8086 (pp30) cc_final: 0.7553 (pp30) REVERT: K 29 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8025 (ttp80) REVERT: K 75 LYS cc_start: 0.8900 (mmtp) cc_final: 0.8674 (mmtp) outliers start: 27 outliers final: 21 residues processed: 259 average time/residue: 0.1163 time to fit residues: 41.9820 Evaluate side-chains 265 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 56 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** 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 = 0.3794 r_free = 0.3794 target = 0.078049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.062492 restraints weight = 53412.828| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.06 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12735 Z= 0.204 Angle : 0.954 39.498 18468 Z= 0.472 Chirality : 0.041 0.415 2105 Planarity : 0.006 0.076 1325 Dihedral : 32.361 88.307 4133 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.39 % Allowed : 40.20 % Favored : 54.41 % 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: 0.63 (0.31), residues: 735 helix: 1.07 (0.23), residues: 525 sheet: None (None), residues: 0 loop : -1.15 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 78 TYR 0.029 0.002 TYR F 88 PHE 0.013 0.002 PHE E 104 HIS 0.011 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00459 (12735) covalent geometry : angle 0.95372 (18468) hydrogen bonds : bond 0.05044 ( 737) hydrogen bonds : angle 3.81679 ( 1844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2204.21 seconds wall clock time: 38 minutes 50.00 seconds (2330.00 seconds total)