Starting phenix.real_space_refine on Wed Aug 5 20:46:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eue_28612/08_2026/8eue_28612_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eue_28612/08_2026/8eue_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_2026/8eue_28612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eue_28612/08_2026/8eue_28612.map" model { file = "/net/cci-nas-00/data/ceres_data/8eue_28612/08_2026/8eue_28612_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eue_28612/08_2026/8eue_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-2.2rc3-6140/lib/python3.11/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: 2.84, per 1000 atoms: 0.24 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: 0.99 Conformation dependent library (CDL) restraints added in 258.3 milliseconds 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: 2.15 Time building geometry restraints manager: 1.33 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=" C3' DT J 53 " pdb=" C2' DT J 53 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.56e+01 bond pdb=" C3' DT I -54 " pdb=" C2' DT I -54 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C1' DT I 18 " pdb=" N1 DT I 18 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.14e+01 bond pdb=" C5' DT I 17 " pdb=" C4' DT I 17 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.14e+01 bond pdb=" C3' DC I -24 " pdb=" O3' DC I -24 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.12e+01 ... (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 - 0.139: 2024 0.139 - 0.278: 75 0.278 - 0.417: 5 0.417 - 0.556: 0 0.556 - 0.695: 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 2.34 1.64 0.70 2.00e-01 2.50e+01 1.21e+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: 7.770 Set stop_for_unknowns flag: 0.010 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.950 Find NCS groups from input model: 0.190 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.008 0.110 12735 Z= 0.612 Angle : 1.430 40.147 18468 Z= 0.967 Chirality : 0.064 0.695 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 are 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/Z covalent geometry : bond 0.00800 / 0.61 (12735) covalent geometry : angle 1.43041 / 0.97 (18468) hydrogen bonds : bond 0.10831 / 6.95 ( 737) hydrogen bonds : angle 5.18973 / 3.72 ( 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 : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7633 (t0) cc_final: 0.6993 (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: 0.8510 (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: 0.8488 (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) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.1268 time to fit residues: 49.1436 Evaluate side-chains 261 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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: 10.0000 chunk 62 optimal weight: 9.9990 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... D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN K 38 ASN K 89 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.079146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.063692 restraints weight = 52790.738| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.15 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 : 0.003 0.046 12735 Z= 0.183 Angle : 0.973 35.612 18468 Z= 0.500 Chirality : 0.052 0.333 2105 Planarity : 0.007 0.083 1325 Dihedral : 33.346 92.656 4133 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.07 % Allowed : 37.09 % Favored : 57.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.28), residues: 735 helix: -0.08 (0.21), residues: 516 sheet: None (None), residues: 0 loop : -1.61 (0.36), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 32 TYR 0.032 0.002 TYR F 88 PHE 0.021 0.002 PHE H 67 HIS 0.010 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.18 (12735) covalent geometry : angle 0.97318 / 0.50 (18468) hydrogen bonds : bond 0.05955 / 3.99 ( 737) hydrogen bonds : angle 4.07333 / 2.89 ( 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 289 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 258 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7821 (m-30) REVERT: D 90 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: E 76 GLN cc_start: 0.8186 (pp30) cc_final: 0.7843 (pp30) REVERT: E 112 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9143 (mp) REVERT: F 40 ARG cc_start: 0.8953 (ttm170) cc_final: 0.8560 (ttm170) REVERT: H 30 ARG cc_start: 0.7758 (mmm160) cc_final: 0.7432 (mmm160) REVERT: H 60 ASN cc_start: 0.9193 (t0) cc_final: 0.8754 (t0) REVERT: H 64 ASN cc_start: 0.8687 (m-40) cc_final: 0.8179 (m110) REVERT: H 73 GLU cc_start: 0.8622 (tp30) cc_final: 0.8420 (tp30) REVERT: H 76 ARG cc_start: 0.8846 (tpt90) cc_final: 0.8593 (tpt90) REVERT: H 92 GLN cc_start: 0.8115 (pp30) cc_final: 0.7503 (pp30) REVERT: K 90 ASP cc_start: 0.8338 (t0) cc_final: 0.7905 (t0) outliers start: 31 outliers final: 18 residues processed: 272 average time/residue: 0.1218 time to fit residues: 46.0830 Evaluate side-chains 267 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 246 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 49 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 Chi-restraints excluded: chain K residue 111 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 98 optimal weight: 0.1980 chunk 97 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.079255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.063714 restraints weight = 53121.603| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.13 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12735 Z= 0.163 Angle : 0.924 36.251 18468 Z= 0.474 Chirality : 0.050 0.362 2105 Planarity : 0.006 0.078 1325 Dihedral : 33.182 91.935 4133 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.90 % Allowed : 36.44 % Favored : 58.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.30), residues: 735 helix: 0.56 (0.22), residues: 517 sheet: None (None), residues: 0 loop : -1.44 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 35 TYR 0.030 0.002 TYR F 88 PHE 0.009 0.001 PHE E 78 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.16 (12735) covalent geometry : angle 0.92444 / 0.47 (18468) hydrogen bonds : bond 0.05568 / 3.75 ( 737) hydrogen bonds : angle 3.83609 / 2.73 ( 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 291 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 261 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8664 (tt) REVERT: A 106 ASP cc_start: 0.8285 (t0) cc_final: 0.7923 (t0) REVERT: D 90 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8362 (mp0) REVERT: E 76 GLN cc_start: 0.8220 (pp30) cc_final: 0.7821 (pp30) REVERT: E 123 ASP cc_start: 0.8103 (m-30) cc_final: 0.7824 (m-30) REVERT: F 39 ARG cc_start: 0.8707 (mmt-90) cc_final: 0.8394 (mmt-90) REVERT: F 85 ASP cc_start: 0.8380 (p0) cc_final: 0.7980 (p0) REVERT: H 60 ASN cc_start: 0.9244 (t0) cc_final: 0.8733 (t0) REVERT: H 64 ASN cc_start: 0.8855 (m-40) cc_final: 0.8317 (m110) REVERT: H 73 GLU cc_start: 0.8715 (tp30) cc_final: 0.8457 (tp30) REVERT: H 76 ARG cc_start: 0.8807 (tpt90) cc_final: 0.8444 (tpt90) REVERT: H 80 TYR cc_start: 0.7436 (t80) cc_final: 0.7187 (t80) REVERT: H 92 GLN cc_start: 0.8129 (pp30) cc_final: 0.7509 (pp30) REVERT: K 29 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8081 (ttp80) outliers start: 30 outliers final: 20 residues processed: 273 average time/residue: 0.1168 time to fit residues: 44.1543 Evaluate side-chains 265 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 242 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 77 ASP Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 51 ILE 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 89 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 57 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 85 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 92 optimal weight: 0.0980 chunk 68 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS ** E 93 GLN ** 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 = 0.3817 r_free = 0.3817 target = 0.079558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.064208 restraints weight = 52665.330| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.09 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12735 Z= 0.156 Angle : 0.922 36.259 18468 Z= 0.466 Chirality : 0.049 0.356 2105 Planarity : 0.006 0.077 1325 Dihedral : 33.075 90.703 4133 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.88 % Allowed : 36.44 % Favored : 57.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.30), residues: 735 helix: 0.73 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -1.23 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 83 TYR 0.035 0.002 TYR F 88 PHE 0.022 0.002 PHE H 67 HIS 0.009 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.16 (12735) covalent geometry : angle 0.92216 / 0.47 (18468) hydrogen bonds : bond 0.05263 / 3.53 ( 737) hydrogen bonds : angle 3.75361 / 2.67 ( 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 310 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 274 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8473 (t0) cc_final: 0.8011 (m-30) REVERT: D 90 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: E 73 GLU cc_start: 0.7672 (mm-30) cc_final: 0.6820 (mm-30) REVERT: E 76 GLN cc_start: 0.8227 (pp30) cc_final: 0.7571 (pp30) REVERT: F 40 ARG cc_start: 0.9006 (ttm170) cc_final: 0.8777 (ttt180) REVERT: F 85 ASP cc_start: 0.8317 (p0) cc_final: 0.8068 (p0) REVERT: H 60 ASN cc_start: 0.9238 (t0) cc_final: 0.8783 (t0) REVERT: H 64 ASN cc_start: 0.8885 (m-40) cc_final: 0.8349 (m-40) REVERT: H 73 GLU cc_start: 0.8717 (tp30) cc_final: 0.8375 (tp30) REVERT: H 76 ARG cc_start: 0.8830 (tpt90) cc_final: 0.8567 (tpt90) REVERT: H 92 GLN cc_start: 0.8146 (pp30) cc_final: 0.7572 (pp30) REVERT: K 29 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8071 (ttp80) REVERT: K 85 LEU cc_start: 0.9091 (mm) cc_final: 0.8760 (mm) REVERT: K 90 ASP cc_start: 0.8304 (t0) cc_final: 0.7924 (t70) outliers start: 36 outliers final: 24 residues processed: 288 average time/residue: 0.1159 time to fit residues: 45.6813 Evaluate side-chains 276 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 250 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 87 SER Chi-restraints excluded: chain A residue 112 ILE 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 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 89 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 86 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 43 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS ** E 93 GLN ** 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 = 0.3814 r_free = 0.3814 target = 0.079345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.063936 restraints weight = 53407.803| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.09 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12735 Z= 0.163 Angle : 0.923 36.308 18468 Z= 0.466 Chirality : 0.049 0.353 2105 Planarity : 0.006 0.078 1325 Dihedral : 33.017 90.107 4133 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.72 % Allowed : 35.78 % Favored : 58.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.30), residues: 735 helix: 0.90 (0.22), residues: 517 sheet: None (None), residues: 0 loop : -1.17 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 78 TYR 0.015 0.001 TYR C 57 PHE 0.009 0.001 PHE E 78 HIS 0.009 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (12735) covalent geometry : angle 0.92293 / 0.47 (18468) hydrogen bonds : bond 0.05356 / 3.59 ( 737) hydrogen bonds : angle 3.76273 / 2.68 ( 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 299 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8502 (t0) cc_final: 0.8095 (m-30) REVERT: A 131 ARG cc_start: 0.8264 (mmt180) cc_final: 0.8016 (mmt180) REVERT: D 90 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8283 (mp0) REVERT: E 73 GLU cc_start: 0.7689 (mm-30) cc_final: 0.6809 (mm-30) REVERT: E 76 GLN cc_start: 0.8280 (pp30) cc_final: 0.7617 (pp30) REVERT: E 105 GLU cc_start: 0.8428 (tt0) cc_final: 0.7786 (tm-30) REVERT: E 112 ILE cc_start: 0.9344 (mp) cc_final: 0.9128 (mp) REVERT: F 39 ARG cc_start: 0.8657 (mmt-90) cc_final: 0.8381 (mmt-90) REVERT: F 40 ARG cc_start: 0.9040 (ttm170) cc_final: 0.8807 (ttt180) REVERT: H 32 GLU cc_start: 0.7620 (tp30) cc_final: 0.7050 (tp30) REVERT: H 59 MET cc_start: 0.8794 (mmm) cc_final: 0.8390 (mmm) REVERT: H 60 ASN cc_start: 0.9220 (t0) cc_final: 0.8782 (t0) REVERT: H 64 ASN cc_start: 0.8917 (m-40) cc_final: 0.8423 (m-40) REVERT: H 73 GLU cc_start: 0.8745 (tp30) cc_final: 0.8384 (tp30) REVERT: H 76 ARG cc_start: 0.8769 (tpt90) cc_final: 0.8559 (tpt90) REVERT: H 84 SER cc_start: 0.8314 (OUTLIER) cc_final: 0.7869 (p) REVERT: H 92 GLN cc_start: 0.8156 (pp30) cc_final: 0.7522 (pp30) REVERT: K 29 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7884 (ttp80) REVERT: K 35 ARG cc_start: 0.8327 (mmp-170) cc_final: 0.8106 (mmm-85) REVERT: K 85 LEU cc_start: 0.9080 (mm) cc_final: 0.8737 (mm) outliers start: 35 outliers final: 25 residues processed: 281 average time/residue: 0.1204 time to fit residues: 46.9146 Evaluate side-chains 284 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 256 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 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 90 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 84 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN F 75 HIS H 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.075179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.060026 restraints weight = 54681.379| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.94 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 12735 Z= 0.252 Angle : 0.986 36.324 18468 Z= 0.501 Chirality : 0.052 0.336 2105 Planarity : 0.007 0.078 1325 Dihedral : 33.096 91.900 4133 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 8.01 % Allowed : 33.66 % Favored : 58.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.30), residues: 735 helix: 0.66 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -1.26 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 78 TYR 0.018 0.002 TYR F 88 PHE 0.038 0.003 PHE A 67 HIS 0.008 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.25 (12735) covalent geometry : angle 0.98562 / 0.50 (18468) hydrogen bonds : bond 0.07754 / 5.23 ( 737) hydrogen bonds : angle 4.13728 / 2.95 ( 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 313 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 264 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8302 (mtm110) cc_final: 0.8082 (mtm-85) REVERT: A 73 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7900 (mm-30) REVERT: A 93 GLN cc_start: 0.9151 (tp40) cc_final: 0.8876 (mm-40) REVERT: A 106 ASP cc_start: 0.8650 (t0) cc_final: 0.8394 (t0) REVERT: C 56 GLU cc_start: 0.8426 (pp20) cc_final: 0.8215 (pp20) REVERT: C 116 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8510 (pp) REVERT: D 57 SER cc_start: 0.9468 (OUTLIER) cc_final: 0.9236 (p) REVERT: D 90 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8289 (mp0) REVERT: E 76 GLN cc_start: 0.8370 (pp30) cc_final: 0.7942 (pp30) REVERT: F 40 ARG cc_start: 0.9140 (ttm170) cc_final: 0.8927 (ttm170) REVERT: H 60 ASN cc_start: 0.9230 (t0) cc_final: 0.8856 (t0) REVERT: H 64 ASN cc_start: 0.8843 (m-40) cc_final: 0.8410 (m-40) REVERT: H 73 GLU cc_start: 0.8776 (tp30) cc_final: 0.8458 (tp30) REVERT: H 76 ARG cc_start: 0.8851 (tpt90) cc_final: 0.8462 (tpt90) REVERT: H 80 TYR cc_start: 0.7504 (t80) cc_final: 0.6995 (t80) REVERT: H 84 SER cc_start: 0.8315 (OUTLIER) cc_final: 0.7956 (p) REVERT: H 92 GLN cc_start: 0.8253 (pp30) cc_final: 0.7556 (pp30) REVERT: K 85 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8803 (mm) REVERT: K 90 ASP cc_start: 0.8224 (t70) cc_final: 0.7807 (t0) outliers start: 49 outliers final: 35 residues processed: 281 average time/residue: 0.1260 time to fit residues: 48.5908 Evaluate side-chains 285 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 87 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 81 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 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 61 SER 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 51 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 85 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 20.0000 chunk 94 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 96 optimal weight: 0.4980 chunk 75 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS ** 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 = 0.3796 r_free = 0.3796 target = 0.078142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.062802 restraints weight = 52729.998| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.06 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12735 Z= 0.160 Angle : 0.947 36.428 18468 Z= 0.474 Chirality : 0.050 0.332 2105 Planarity : 0.006 0.077 1325 Dihedral : 33.065 89.145 4133 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.07 % Allowed : 37.25 % Favored : 57.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.31), residues: 735 helix: 0.99 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.11 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 35 TYR 0.030 0.002 TYR F 88 PHE 0.012 0.001 PHE D 62 HIS 0.009 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (12735) covalent geometry : angle 0.94672 / 0.47 (18468) hydrogen bonds : bond 0.05270 / 3.54 ( 737) hydrogen bonds : angle 3.79005 / 2.70 ( 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 301 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 270 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8222 (mtm110) cc_final: 0.7615 (mtm-85) REVERT: A 73 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7838 (mm-30) REVERT: A 93 GLN cc_start: 0.9112 (tp40) cc_final: 0.8383 (mm-40) REVERT: A 97 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8209 (mp0) REVERT: A 106 ASP cc_start: 0.8662 (t0) cc_final: 0.8394 (t0) REVERT: C 116 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8428 (pp) REVERT: D 57 SER cc_start: 0.9369 (m) cc_final: 0.9150 (p) REVERT: D 90 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8303 (mp0) REVERT: E 76 GLN cc_start: 0.8293 (pp30) cc_final: 0.7854 (pp30) REVERT: E 133 GLU cc_start: 0.8244 (mp0) cc_final: 0.7708 (mp0) REVERT: F 39 ARG cc_start: 0.8774 (mmt-90) cc_final: 0.8524 (mmt-90) REVERT: H 32 GLU cc_start: 0.7626 (tp30) cc_final: 0.7227 (tp30) REVERT: H 92 GLN cc_start: 0.8148 (pp30) cc_final: 0.7533 (pp30) REVERT: K 29 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8011 (ttp80) REVERT: K 85 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8769 (mm) outliers start: 31 outliers final: 24 residues processed: 285 average time/residue: 0.1177 time to fit residues: 46.1005 Evaluate side-chains 283 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 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 107 VAL Chi-restraints excluded: chain C residue 116 LEU 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 51 ILE Chi-restraints excluded: chain E residue 57 SER 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 96 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 85 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 51 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 81 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 HIS ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN H 60 ASN H 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.078290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.062822 restraints weight = 52986.647| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.08 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12735 Z= 0.164 Angle : 0.940 36.381 18468 Z= 0.472 Chirality : 0.049 0.340 2105 Planarity : 0.006 0.076 1325 Dihedral : 32.980 88.448 4133 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.90 % Allowed : 38.40 % Favored : 56.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.31), residues: 735 helix: 0.99 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -1.06 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 78 TYR 0.022 0.002 TYR D 37 PHE 0.009 0.001 PHE D 62 HIS 0.010 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (12735) covalent geometry : angle 0.94012 / 0.47 (18468) hydrogen bonds : bond 0.05344 / 3.58 ( 737) hydrogen bonds : angle 3.79786 / 2.72 ( 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 298 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 268 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8267 (mtm110) cc_final: 0.7659 (mtm-85) REVERT: A 73 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7870 (mm-30) REVERT: A 93 GLN cc_start: 0.9109 (tp40) cc_final: 0.8731 (mm-40) REVERT: D 57 SER cc_start: 0.9433 (m) cc_final: 0.9196 (p) REVERT: D 90 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8294 (mp0) REVERT: E 76 GLN cc_start: 0.8317 (pp30) cc_final: 0.7867 (pp30) REVERT: E 133 GLU cc_start: 0.8252 (mp0) cc_final: 0.7546 (mp0) REVERT: H 32 GLU cc_start: 0.7592 (tp30) cc_final: 0.7167 (tp30) REVERT: H 64 ASN cc_start: 0.8745 (m110) cc_final: 0.8359 (m110) REVERT: H 80 TYR cc_start: 0.7188 (t80) cc_final: 0.6689 (t80) REVERT: H 96 ARG cc_start: 0.8815 (mmt-90) cc_final: 0.8562 (mmt-90) REVERT: K 29 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7928 (ttp80) outliers start: 30 outliers final: 23 residues processed: 283 average time/residue: 0.1220 time to fit residues: 47.4181 Evaluate side-chains 281 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 256 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 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 107 VAL 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 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 96 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 0.0570 chunk 57 optimal weight: 0.5980 chunk 82 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3809 r_free = 0.3809 target = 0.078975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.063466 restraints weight = 52764.813| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.05 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12735 Z= 0.163 Angle : 0.951 36.423 18468 Z= 0.476 Chirality : 0.050 0.407 2105 Planarity : 0.006 0.076 1325 Dihedral : 32.907 88.302 4133 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.90 % Allowed : 39.22 % Favored : 55.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.31), residues: 735 helix: 1.03 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.02 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 78 TYR 0.022 0.002 TYR F 88 PHE 0.008 0.001 PHE E 104 HIS 0.011 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (12735) covalent geometry : angle 0.95139 / 0.48 (18468) hydrogen bonds : bond 0.05157 / 3.45 ( 737) hydrogen bonds : angle 3.80706 / 2.71 ( 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 295 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9142 (tp-100) cc_final: 0.8912 (tp-100) REVERT: A 93 GLN cc_start: 0.9096 (tp40) cc_final: 0.8749 (mm-40) REVERT: C 61 GLU cc_start: 0.8011 (mp0) cc_final: 0.7786 (mp0) REVERT: D 57 SER cc_start: 0.9427 (m) cc_final: 0.9195 (p) REVERT: E 76 GLN cc_start: 0.8302 (pp30) cc_final: 0.7848 (pp30) REVERT: E 105 GLU cc_start: 0.8395 (tt0) cc_final: 0.7764 (tm-30) REVERT: E 133 GLU cc_start: 0.8237 (mp0) cc_final: 0.7493 (mp0) REVERT: H 32 GLU cc_start: 0.7559 (tp30) cc_final: 0.7139 (tp30) REVERT: H 64 ASN cc_start: 0.8732 (m110) cc_final: 0.8354 (m-40) REVERT: H 73 GLU cc_start: 0.8686 (tp30) cc_final: 0.8371 (tp30) REVERT: H 80 TYR cc_start: 0.7243 (t80) cc_final: 0.6621 (t80) REVERT: H 84 SER cc_start: 0.8293 (OUTLIER) cc_final: 0.7929 (p) REVERT: H 89 ARG cc_start: 0.7517 (ptm160) cc_final: 0.7252 (ptm160) REVERT: H 92 GLN cc_start: 0.8394 (pp30) cc_final: 0.7636 (pp30) REVERT: K 29 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.7994 (ttp80) outliers start: 30 outliers final: 24 residues processed: 281 average time/residue: 0.1131 time to fit residues: 43.8290 Evaluate side-chains 284 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 258 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 82 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 39 ARG 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 107 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 84 SER 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 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3804 r_free = 0.3804 target = 0.078574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.063079 restraints weight = 53395.650| |-----------------------------------------------------------------------------| 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: 0.8059 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12735 Z= 0.168 Angle : 0.952 36.419 18468 Z= 0.477 Chirality : 0.049 0.337 2105 Planarity : 0.006 0.075 1325 Dihedral : 32.859 88.559 4133 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.41 % Allowed : 39.87 % Favored : 55.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.31), residues: 735 helix: 1.03 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.10 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 89 TYR 0.023 0.002 TYR F 88 PHE 0.008 0.001 PHE E 104 HIS 0.011 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (12735) covalent geometry : angle 0.95215 / 0.48 (18468) hydrogen bonds : bond 0.05278 / 3.53 ( 737) hydrogen bonds : angle 3.82346 / 2.72 ( 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 289 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 262 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9136 (tp-100) cc_final: 0.8857 (tp-100) REVERT: A 73 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7893 (mm-30) REVERT: A 93 GLN cc_start: 0.9089 (tp40) cc_final: 0.8743 (mm-40) REVERT: C 104 GLN cc_start: 0.8670 (mp10) cc_final: 0.8445 (mp10) REVERT: D 57 SER cc_start: 0.9426 (m) cc_final: 0.9207 (p) REVERT: D 90 GLU cc_start: 0.8551 (mp0) cc_final: 0.7564 (mp0) REVERT: E 60 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7617 (tt) REVERT: E 76 GLN cc_start: 0.8315 (pp30) cc_final: 0.7851 (pp30) REVERT: E 105 GLU cc_start: 0.8371 (tt0) cc_final: 0.7721 (tm-30) REVERT: E 133 GLU cc_start: 0.8214 (mp0) cc_final: 0.7465 (mp0) REVERT: H 32 GLU cc_start: 0.7558 (tp30) cc_final: 0.7129 (tp30) REVERT: H 64 ASN cc_start: 0.8748 (m110) cc_final: 0.8357 (m110) REVERT: H 73 GLU cc_start: 0.8711 (tp30) cc_final: 0.8445 (tp30) REVERT: H 80 TYR cc_start: 0.7227 (t80) cc_final: 0.6590 (t80) REVERT: H 84 SER cc_start: 0.8289 (OUTLIER) cc_final: 0.7929 (p) REVERT: H 92 GLN cc_start: 0.8395 (pp30) cc_final: 0.7729 (pp30) REVERT: K 29 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8015 (ttp80) outliers start: 27 outliers final: 23 residues processed: 277 average time/residue: 0.1057 time to fit residues: 40.6424 Evaluate side-chains 287 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 261 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 82 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 39 ARG 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 107 VAL Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 84 SER 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: 0.6980 chunk 91 optimal weight: 0.0970 chunk 62 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 9 optimal weight: 0.0020 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3827 r_free = 0.3827 target = 0.079846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.064407 restraints weight = 52737.070| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.08 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12735 Z= 0.158 Angle : 0.963 36.495 18468 Z= 0.478 Chirality : 0.049 0.336 2105 Planarity : 0.006 0.086 1325 Dihedral : 32.772 87.882 4133 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.74 % Allowed : 39.22 % 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 are not related in a simple way. whole: 0.52 (0.31), residues: 735 helix: 0.98 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.10 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 81 TYR 0.028 0.002 TYR F 88 PHE 0.009 0.001 PHE E 104 HIS 0.012 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (12735) covalent geometry : angle 0.96317 / 0.48 (18468) hydrogen bonds : bond 0.04892 / 3.26 ( 737) hydrogen bonds : angle 3.76982 / 2.69 ( 1844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2128.35 seconds wall clock time: 37 minutes 21.08 seconds (2241.08 seconds total)