Starting phenix.real_space_refine on Fri Jul 3 12:57:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sn7_40615/07_2026/8sn7_40615.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sn7_40615/07_2026/8sn7_40615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sn7_40615/07_2026/8sn7_40615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sn7_40615/07_2026/8sn7_40615.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8sn7_40615/07_2026/8sn7_40615.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sn7_40615/07_2026/8sn7_40615.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sn7_40615/07_2026/8sn7_40615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sn7_40615/07_2026/8sn7_40615.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 294 5.49 5 S 33 5.16 5 C 8269 2.51 5 N 2713 2.21 5 O 3289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14600 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Conformer: "B" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} bond proxies already assigned to first conformer: 698 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1188 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12296 SG CYS K 31 33.174 72.290 48.380 1.00 72.35 S ATOM 12446 SG CYS K 51 31.114 69.178 47.704 1.00 73.71 S ATOM 12470 SG CYS K 54 32.901 70.989 44.890 1.00 79.16 S ATOM 12187 SG CYS K 16 22.600 66.502 53.978 1.00 79.23 S ATOM 12205 SG CYS K 19 20.009 64.339 55.691 1.00 76.33 S ATOM 12335 SG CYS K 36 23.168 65.453 57.650 1.00 74.99 S ATOM 12357 SG CYS K 39 23.514 62.918 55.146 1.00 76.41 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 residue: pdb=" N ARG M 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG M 74 " occ=0.45 residue: pdb=" N GLY M 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.25 residue: pdb=" N GLY M 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY M 76 " occ=0.25 Time building chain proxies: 3.32, per 1000 atoms: 0.23 Number of scatterers: 14600 At special positions: 0 Unit cell: (110.224, 131.472, 127.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 33 16.00 P 294 15.00 O 3289 8.00 N 2713 7.00 C 8269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " SER C 124 " - " SER D 123 " " SER G-102 " - " SER H 123 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 552.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " Number of angles added : 9 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 62.9% alpha, 4.5% beta 136 base pairs and 244 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.543A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.683A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.919A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 129 through 134 removed outlier: 3.864A pdb=" N ALA C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 150 Processing helix chain 'C' and resid 159 through 186 removed outlier: 3.548A pdb=" N LEU C 178 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 202 Processing helix chain 'C' and resid 203 through 210 Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.795A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.602A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.697A 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 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 4.006A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.833A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.635A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid -97 through -92 Processing helix chain 'G' and resid -86 through -76 Processing helix chain 'G' and resid -67 through -40 Processing helix chain 'G' and resid -34 through -23 removed outlier: 3.658A pdb=" N ASP G -23 " --> pdb=" O ALA G -27 " (cutoff:3.500A) Processing helix chain 'G' and resid -22 through -16 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.549A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.650A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.730A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 15 removed outlier: 3.895A pdb=" N GLN K 15 " --> pdb=" O LEU K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 47 Processing helix chain 'K' and resid 58 through 69 removed outlier: 3.861A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 90 removed outlier: 3.567A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 removed outlier: 3.676A pdb=" N ARG L 5 " --> pdb=" O MET L 1 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP L 16 " --> pdb=" O ASP L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 91 removed outlier: 4.132A pdb=" N ARG L 90 " --> pdb=" O LEU L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.575A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 143 removed outlier: 3.968A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 34 Processing helix chain 'M' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.099A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 155 through 156 removed outlier: 8.078A pdb=" N ARG C 155 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 190 through 191 Processing sheet with id=AA6, first strand: chain 'C' and resid 214 through 215 removed outlier: 7.013A pdb=" N THR C 214 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.205A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid -71 through -70 removed outlier: 7.725A pdb=" N ARG G -71 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 27 through 28 removed outlier: 3.558A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 24 Processing sheet with id=AB3, first strand: chain 'M' and resid 5 through 6 491 hydrogen bonds defined for protein. 1437 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 349 hydrogen bonds 694 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 244 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3222 1.33 - 1.45: 4431 1.45 - 1.57: 7184 1.57 - 1.69: 586 1.69 - 1.81: 49 Bond restraints: 15472 Sorted by residual: bond pdb=" C3' DA J -73 " pdb=" C2' DA J -73 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.28e+01 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DA I -22 " pdb=" C2' DA I -22 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.22e+00 bond pdb=" C3' DC I 0 " pdb=" C2' DC I 0 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.12e+00 ... (remaining 15467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 21002 1.56 - 3.12: 1106 3.12 - 4.68: 41 4.68 - 6.24: 15 6.24 - 7.80: 7 Bond angle restraints: 22171 Sorted by residual: angle pdb=" O4' DT I -26 " pdb=" C4' DT I -26 " pdb=" C3' DT I -26 " ideal model delta sigma weight residual 106.00 102.92 3.08 6.00e-01 2.78e+00 2.63e+01 angle pdb=" O4' DC J -71 " pdb=" C4' DC J -71 " pdb=" C3' DC J -71 " ideal model delta sigma weight residual 106.00 103.04 2.96 6.00e-01 2.78e+00 2.43e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.68 -2.78 6.00e-01 2.78e+00 2.14e+01 angle pdb=" N3 DT I 38 " pdb=" C4 DT I 38 " pdb=" O4 DT I 38 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT I -17 " pdb=" C4 DT I -17 " pdb=" O4 DT I -17 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.91e+01 ... (remaining 22166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 7274 35.74 - 71.48: 1319 71.48 - 107.22: 16 107.22 - 142.96: 0 142.96 - 178.70: 2 Dihedral angle restraints: 8611 sinusoidal: 5471 harmonic: 3140 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 41.30 178.70 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 70.18 149.82 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" CB GLU D 105 " pdb=" CG GLU D 105 " pdb=" CD GLU D 105 " pdb=" OE1 GLU D 105 " ideal model delta sinusoidal sigma weight residual 0.00 89.83 -89.83 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 8608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1478 0.032 - 0.065: 670 0.065 - 0.097: 240 0.097 - 0.129: 120 0.129 - 0.162: 8 Chirality restraints: 2516 Sorted by residual: chirality pdb=" CG LEU F 62 " pdb=" CB LEU F 62 " pdb=" CD1 LEU F 62 " pdb=" CD2 LEU F 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" CA ASN K 32 " pdb=" N ASN K 32 " pdb=" C ASN K 32 " pdb=" CB ASN K 32 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 2513 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 60 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO L 61 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO L 61 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO L 61 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS K 37 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO K 38 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO K 38 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO K 38 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.027 2.00e-02 2.50e+03 1.15e-02 3.66e+00 pdb=" N9 DA I -35 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " 0.003 2.00e-02 2.50e+03 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1637 2.75 - 3.29: 13071 3.29 - 3.82: 27060 3.82 - 4.36: 31252 4.36 - 4.90: 46874 Nonbonded interactions: 119894 Sorted by model distance: nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.210 2.496 nonbonded pdb=" OG SER L 138 " pdb=" NH1 ARG L 139 " model vdw 2.261 3.120 nonbonded pdb=" O PRO L 40 " pdb=" OG SER L 43 " model vdw 2.285 3.040 nonbonded pdb=" O TYR C 152 " pdb=" OG SER D 78 " model vdw 2.294 3.040 nonbonded pdb=" O ARG L 125 " pdb=" OG1 THR L 129 " model vdw 2.300 3.040 ... (remaining 119889 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid -102 through 5) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.230 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 20.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 15482 Z= 0.477 Angle : 0.712 8.823 22186 Z= 0.604 Chirality : 0.045 0.162 2516 Planarity : 0.004 0.073 1794 Dihedral : 25.759 178.704 6577 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.83 (0.26), residues: 1057 helix: 2.34 (0.21), residues: 627 sheet: -1.13 (0.72), residues: 41 loop : -0.41 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 125 TYR 0.025 0.002 TYR M 59 PHE 0.008 0.001 PHE E 78 TRP 0.007 0.001 TRP K 77 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.48 (15472) covalent geometry : angle 0.70823 / 0.60 (22171) hydrogen bonds : bond 0.10596 / 6.66 ( 840) hydrogen bonds : angle 4.21654 / 2.94 ( 2131) metal coordination : bond 0.00765 / 0.37 ( 8) metal coordination : angle 3.87919 / 1.75 ( 9) link_TRANS : bond 0.00083 / 0.04 ( 2) link_TRANS : angle 0.23139 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 LYS cc_start: 0.8814 (ttpp) cc_final: 0.8564 (ttmm) REVERT: E 76 GLN cc_start: 0.8261 (pp30) cc_final: 0.8002 (pp30) REVERT: H 34 LYS cc_start: 0.9132 (mtmm) cc_final: 0.8899 (mtmm) REVERT: H 86 ARG cc_start: 0.8111 (mmt90) cc_final: 0.7803 (mmt-90) REVERT: H 120 LYS cc_start: 0.9090 (ttpt) cc_final: 0.8569 (ttpp) REVERT: L 63 LYS cc_start: 0.8597 (mmtp) cc_final: 0.8253 (mttt) REVERT: L 114 ASN cc_start: 0.7881 (t0) cc_final: 0.7667 (m-40) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1423 time to fit residues: 44.2080 Evaluate side-chains 189 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN F 25 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.083894 restraints weight = 42426.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.085711 restraints weight = 23092.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.086819 restraints weight = 16731.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.086957 restraints weight = 15290.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.087032 restraints weight = 13959.349| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (9 function evaluations) r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15482 Z= 0.172 Angle : 0.645 11.703 22186 Z= 0.367 Chirality : 0.043 0.230 2516 Planarity : 0.005 0.052 1794 Dihedral : 29.084 179.202 4413 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.08 % Allowed : 10.17 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.80 (0.26), residues: 1057 helix: 2.33 (0.21), residues: 644 sheet: -1.46 (0.70), residues: 42 loop : -0.54 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 92 TYR 0.035 0.002 TYR L 134 PHE 0.013 0.001 PHE L 62 TRP 0.019 0.002 TRP L 33 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (15472) covalent geometry : angle 0.63765 / 0.37 (22171) hydrogen bonds : bond 0.05664 / 3.77 ( 840) hydrogen bonds : angle 3.76920 / 2.60 ( 2131) metal coordination : bond 0.00574 / 0.26 ( 8) metal coordination : angle 4.82495 / 2.05 ( 9) link_TRANS : bond 0.00069 / 0.04 ( 2) link_TRANS : angle 0.50268 / 0.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 0.410 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: symmetry clash REVERT: D 116 LYS cc_start: 0.8877 (ttpp) cc_final: 0.8446 (ttmm) REVERT: E 76 GLN cc_start: 0.8289 (pp30) cc_final: 0.7996 (pp30) REVERT: E 120 MET cc_start: 0.8367 (mtp) cc_final: 0.8103 (mtt) REVERT: H 34 LYS cc_start: 0.9220 (mtmm) cc_final: 0.8929 (mtmm) REVERT: H 86 ARG cc_start: 0.8199 (mmt90) cc_final: 0.7919 (mmt-90) REVERT: H 120 LYS cc_start: 0.9106 (ttpt) cc_final: 0.8548 (ttpt) REVERT: L 63 LYS cc_start: 0.8416 (mmtp) cc_final: 0.8048 (mttt) REVERT: L 127 TYR cc_start: 0.7998 (t80) cc_final: 0.7325 (t80) REVERT: L 133 LYS cc_start: 0.8775 (mmmt) cc_final: 0.8325 (mmmt) REVERT: L 136 ARG cc_start: 0.9378 (pmt-80) cc_final: 0.8923 (pmt-80) outliers start: 10 outliers final: 7 residues processed: 198 average time/residue: 0.1446 time to fit residues: 40.0570 Evaluate side-chains 193 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 186 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain G residue -95 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain M residue 13 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 33 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN L 32 HIS L 92 GLN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.083753 restraints weight = 37566.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.085454 restraints weight = 21332.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.086712 restraints weight = 16052.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.086682 restraints weight = 14655.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.086841 restraints weight = 13215.226| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15482 Z= 0.160 Angle : 0.625 15.500 22186 Z= 0.355 Chirality : 0.042 0.230 2516 Planarity : 0.005 0.060 1794 Dihedral : 29.238 179.028 4413 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.06 % Allowed : 11.69 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.86 (0.27), residues: 1057 helix: 2.40 (0.21), residues: 649 sheet: -1.50 (0.68), residues: 38 loop : -0.59 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 72 TYR 0.021 0.002 TYR L 134 PHE 0.011 0.001 PHE L 50 TRP 0.034 0.003 TRP L 33 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (15472) covalent geometry : angle 0.61259 / 0.35 (22171) hydrogen bonds : bond 0.05273 / 3.52 ( 840) hydrogen bonds : angle 3.65759 / 2.53 ( 2131) metal coordination : bond 0.00706 / 0.39 ( 8) metal coordination : angle 6.09801 / 2.69 ( 9) link_TRANS : bond 0.00113 / 0.06 ( 2) link_TRANS : angle 0.47156 / 0.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.406 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: symmetry clash REVERT: E 59 GLU cc_start: 0.8505 (pm20) cc_final: 0.8278 (pm20) REVERT: E 76 GLN cc_start: 0.8425 (pp30) cc_final: 0.7986 (pp30) REVERT: E 120 MET cc_start: 0.8399 (mtp) cc_final: 0.8152 (mtt) REVERT: F 25 ASN cc_start: 0.9358 (OUTLIER) cc_final: 0.9114 (t0) REVERT: G -38 LYS cc_start: 0.8989 (mmmm) cc_final: 0.8721 (mmmm) REVERT: H 34 LYS cc_start: 0.9219 (mtmm) cc_final: 0.8932 (mtmm) REVERT: H 86 ARG cc_start: 0.8217 (mmt90) cc_final: 0.7945 (mmt-90) REVERT: H 120 LYS cc_start: 0.9086 (ttpt) cc_final: 0.8515 (ttpt) REVERT: L 63 LYS cc_start: 0.8428 (mmtp) cc_final: 0.8074 (mttt) REVERT: L 72 ARG cc_start: 0.6856 (ttt180) cc_final: 0.6318 (ttt180) REVERT: L 127 TYR cc_start: 0.7768 (t80) cc_final: 0.7340 (t80) REVERT: L 133 LYS cc_start: 0.8746 (mmmt) cc_final: 0.8363 (mmmt) REVERT: L 136 ARG cc_start: 0.9408 (pmt-80) cc_final: 0.8997 (pmt-80) REVERT: L 147 MET cc_start: 0.8675 (mpp) cc_final: 0.8348 (mpp) outliers start: 19 outliers final: 11 residues processed: 200 average time/residue: 0.1427 time to fit residues: 40.1686 Evaluate side-chains 199 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue -102 SER Chi-restraints excluded: chain G residue -95 SER Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain M residue 13 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 92 GLN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.083595 restraints weight = 48639.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.085511 restraints weight = 26018.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.085555 restraints weight = 18094.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.086120 restraints weight = 16134.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.086211 restraints weight = 16169.376| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15482 Z= 0.167 Angle : 0.631 16.189 22186 Z= 0.353 Chirality : 0.043 0.252 2516 Planarity : 0.005 0.055 1794 Dihedral : 29.400 178.447 4413 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.95 % Allowed : 12.66 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.84 (0.27), residues: 1057 helix: 2.43 (0.21), residues: 643 sheet: -1.44 (0.78), residues: 34 loop : -0.69 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 63 TYR 0.026 0.002 TYR K 84 PHE 0.017 0.001 PHE L 62 TRP 0.035 0.003 TRP L 33 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (15472) covalent geometry : angle 0.61779 / 0.35 (22171) hydrogen bonds : bond 0.05263 / 3.51 ( 840) hydrogen bonds : angle 3.64066 / 2.52 ( 2131) metal coordination : bond 0.00833 / 0.38 ( 8) metal coordination : angle 6.38334 / 2.82 ( 9) link_TRANS : bond 0.00116 / 0.06 ( 2) link_TRANS : angle 0.44064 / 0.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.410 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: E 59 GLU cc_start: 0.8486 (pm20) cc_final: 0.8196 (pm20) REVERT: E 76 GLN cc_start: 0.8472 (pp30) cc_final: 0.8009 (pp30) REVERT: E 94 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8433 (mm-30) REVERT: G -38 LYS cc_start: 0.8982 (mmmm) cc_final: 0.8738 (mmmm) REVERT: H 34 LYS cc_start: 0.9274 (mtmm) cc_final: 0.8944 (mtmm) REVERT: H 86 ARG cc_start: 0.8240 (mmt90) cc_final: 0.7965 (mmt-90) REVERT: H 120 LYS cc_start: 0.9072 (ttpt) cc_final: 0.8487 (ttpt) REVERT: L 63 LYS cc_start: 0.8537 (mmtp) cc_final: 0.8172 (mttt) REVERT: L 127 TYR cc_start: 0.7785 (t80) cc_final: 0.7534 (t80) REVERT: L 133 LYS cc_start: 0.8654 (mmmt) cc_final: 0.8339 (mmmt) REVERT: L 136 ARG cc_start: 0.9369 (pmt-80) cc_final: 0.8991 (pmt-80) REVERT: L 147 MET cc_start: 0.8632 (mpp) cc_final: 0.8345 (mpp) REVERT: M 71 LEU cc_start: 0.9133 (mt) cc_final: 0.8927 (mp) outliers start: 18 outliers final: 15 residues processed: 197 average time/residue: 0.1462 time to fit residues: 40.2143 Evaluate side-chains 204 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 189 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue -102 SER Chi-restraints excluded: chain G residue -95 SER Chi-restraints excluded: chain G residue -13 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 86 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 126 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.129745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.074665 restraints weight = 42176.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.077336 restraints weight = 20514.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.079025 restraints weight = 13696.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.080039 restraints weight = 11071.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.080459 restraints weight = 9943.307| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15482 Z= 0.151 Angle : 0.616 14.360 22186 Z= 0.346 Chirality : 0.042 0.250 2516 Planarity : 0.004 0.056 1794 Dihedral : 29.463 178.360 4413 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.38 % Allowed : 13.85 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.92 (0.27), residues: 1057 helix: 2.44 (0.21), residues: 646 sheet: -1.13 (0.82), residues: 33 loop : -0.60 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 125 TYR 0.016 0.002 TYR K 84 PHE 0.017 0.001 PHE L 51 TRP 0.024 0.002 TRP L 33 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (15472) covalent geometry : angle 0.60519 / 0.34 (22171) hydrogen bonds : bond 0.05049 / 3.36 ( 840) hydrogen bonds : angle 3.55042 / 2.45 ( 2131) metal coordination : bond 0.00629 / 0.28 ( 8) metal coordination : angle 5.75622 / 2.54 ( 9) link_TRANS : bond 0.00094 / 0.05 ( 2) link_TRANS : angle 0.43326 / 0.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.421 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: C 205 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8239 (mm-30) REVERT: E 59 GLU cc_start: 0.8597 (pm20) cc_final: 0.8228 (pm20) REVERT: E 76 GLN cc_start: 0.8479 (pp30) cc_final: 0.8025 (pp30) REVERT: E 94 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8423 (mm-30) REVERT: G -38 LYS cc_start: 0.8972 (mmmm) cc_final: 0.8710 (mmmm) REVERT: H 34 LYS cc_start: 0.9271 (mtmm) cc_final: 0.8923 (mtmm) REVERT: H 86 ARG cc_start: 0.8258 (mmt90) cc_final: 0.8004 (mmt-90) REVERT: H 120 LYS cc_start: 0.9040 (ttpt) cc_final: 0.8439 (ttpt) REVERT: L 63 LYS cc_start: 0.8416 (mmtp) cc_final: 0.8071 (mttt) REVERT: L 127 TYR cc_start: 0.7833 (t80) cc_final: 0.7572 (t80) REVERT: L 133 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8353 (mmmt) REVERT: L 136 ARG cc_start: 0.9386 (pmt-80) cc_final: 0.8960 (pmt-80) REVERT: L 147 MET cc_start: 0.8735 (mpp) cc_final: 0.8476 (mpp) outliers start: 22 outliers final: 16 residues processed: 195 average time/residue: 0.1411 time to fit residues: 38.7095 Evaluate side-chains 203 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue -102 SER Chi-restraints excluded: chain G residue -95 SER Chi-restraints excluded: chain G residue -13 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 86 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 107 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.080132 restraints weight = 41740.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.081509 restraints weight = 24728.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.081785 restraints weight = 19488.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.082958 restraints weight = 16480.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.082745 restraints weight = 16128.721| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15482 Z= 0.155 Angle : 0.628 14.014 22186 Z= 0.349 Chirality : 0.042 0.244 2516 Planarity : 0.004 0.052 1794 Dihedral : 29.531 178.243 4413 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.49 % Allowed : 14.39 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.90 (0.27), residues: 1057 helix: 2.43 (0.21), residues: 646 sheet: -1.08 (0.84), residues: 33 loop : -0.61 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 125 TYR 0.028 0.002 TYR L 134 PHE 0.023 0.001 PHE L 62 TRP 0.031 0.003 TRP L 33 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (15472) covalent geometry : angle 0.61807 / 0.35 (22171) hydrogen bonds : bond 0.05035 / 3.35 ( 840) hydrogen bonds : angle 3.52494 / 2.43 ( 2131) metal coordination : bond 0.00728 / 0.35 ( 8) metal coordination : angle 5.63948 / 2.49 ( 9) link_TRANS : bond 0.00095 / 0.05 ( 2) link_TRANS : angle 0.41625 / 0.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.352 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: C 205 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8285 (mm-30) REVERT: E 59 GLU cc_start: 0.8560 (pm20) cc_final: 0.8192 (pm20) REVERT: E 76 GLN cc_start: 0.8407 (pp30) cc_final: 0.7967 (pp30) REVERT: E 94 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8441 (mm-30) REVERT: G -38 LYS cc_start: 0.8938 (mmmm) cc_final: 0.8726 (mmmm) REVERT: H 34 LYS cc_start: 0.9285 (mtmm) cc_final: 0.8949 (mtmm) REVERT: H 86 ARG cc_start: 0.8230 (mmt90) cc_final: 0.7964 (mmt-90) REVERT: H 120 LYS cc_start: 0.9042 (ttpt) cc_final: 0.8477 (ttpt) REVERT: L 33 TRP cc_start: 0.8098 (m100) cc_final: 0.7118 (m100) REVERT: L 63 LYS cc_start: 0.8502 (mmtp) cc_final: 0.8140 (mttt) REVERT: L 125 ARG cc_start: 0.8846 (mtm110) cc_final: 0.8615 (ptt-90) REVERT: L 136 ARG cc_start: 0.9363 (pmt-80) cc_final: 0.9135 (pmt-80) REVERT: L 147 MET cc_start: 0.8763 (mpp) cc_final: 0.8520 (mpp) outliers start: 23 outliers final: 18 residues processed: 200 average time/residue: 0.1276 time to fit residues: 36.1738 Evaluate side-chains 202 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue -102 SER Chi-restraints excluded: chain G residue -95 SER Chi-restraints excluded: chain G residue -13 VAL Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 86 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 37 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 94 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 46 GLN L 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.132975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.080301 restraints weight = 43464.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.081602 restraints weight = 23710.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.082180 restraints weight = 16579.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.082628 restraints weight = 14756.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.082809 restraints weight = 14524.904| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15482 Z= 0.145 Angle : 0.614 13.099 22186 Z= 0.343 Chirality : 0.041 0.254 2516 Planarity : 0.004 0.048 1794 Dihedral : 29.552 178.018 4413 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.49 % Allowed : 15.48 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.96 (0.27), residues: 1057 helix: 2.45 (0.21), residues: 646 sheet: -1.01 (0.85), residues: 33 loop : -0.56 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 125 TYR 0.021 0.002 TYR L 134 PHE 0.020 0.001 PHE L 51 TRP 0.029 0.003 TRP L 141 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 (15472) covalent geometry : angle 0.60497 / 0.34 (22171) hydrogen bonds : bond 0.04868 / 3.23 ( 840) hydrogen bonds : angle 3.45901 / 2.38 ( 2131) metal coordination : bond 0.00687 / 0.32 ( 8) metal coordination : angle 5.36714 / 2.35 ( 9) link_TRANS : bond 0.00079 / 0.04 ( 2) link_TRANS : angle 0.38677 / 0.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.396 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 59 GLU cc_start: 0.8752 (pm20) cc_final: 0.8380 (pm20) REVERT: C 205 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8287 (mm-30) REVERT: E 59 GLU cc_start: 0.8549 (pm20) cc_final: 0.8237 (pm20) REVERT: E 76 GLN cc_start: 0.8525 (pp30) cc_final: 0.8103 (pp30) REVERT: E 94 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8434 (mm-30) REVERT: G -38 LYS cc_start: 0.8917 (mmmm) cc_final: 0.8716 (mmmm) REVERT: H 34 LYS cc_start: 0.9258 (mtmm) cc_final: 0.8947 (mtmm) REVERT: H 86 ARG cc_start: 0.8230 (mmt90) cc_final: 0.7976 (mmt-90) REVERT: H 120 LYS cc_start: 0.9028 (ttpt) cc_final: 0.8441 (ttpt) REVERT: L 33 TRP cc_start: 0.8182 (m100) cc_final: 0.7153 (m100) REVERT: L 63 LYS cc_start: 0.8464 (mmtp) cc_final: 0.8123 (mttt) REVERT: L 101 LYS cc_start: 0.9350 (mmmt) cc_final: 0.9147 (mmmm) REVERT: L 125 ARG cc_start: 0.8907 (mtm110) cc_final: 0.8544 (ptp-170) REVERT: L 136 ARG cc_start: 0.9377 (pmt-80) cc_final: 0.9081 (pmt-80) REVERT: L 147 MET cc_start: 0.8631 (mpp) cc_final: 0.8390 (mpp) outliers start: 23 outliers final: 20 residues processed: 197 average time/residue: 0.1340 time to fit residues: 37.3100 Evaluate side-chains 205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue -102 SER Chi-restraints excluded: chain G residue -95 SER Chi-restraints excluded: chain G residue -13 VAL Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 127 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 46 GLN ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.132452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.080116 restraints weight = 47139.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.081234 restraints weight = 24754.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.083162 restraints weight = 16505.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.083027 restraints weight = 15473.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.082843 restraints weight = 13744.381| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15482 Z= 0.167 Angle : 0.633 13.468 22186 Z= 0.349 Chirality : 0.042 0.237 2516 Planarity : 0.005 0.061 1794 Dihedral : 29.605 177.960 4413 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.27 % Allowed : 16.34 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.91 (0.27), residues: 1057 helix: 2.42 (0.21), residues: 646 sheet: -1.15 (0.82), residues: 33 loop : -0.56 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 125 TYR 0.017 0.002 TYR L 134 PHE 0.029 0.002 PHE L 50 TRP 0.027 0.003 TRP L 33 HIS 0.004 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (15472) covalent geometry : angle 0.62371 / 0.35 (22171) hydrogen bonds : bond 0.05059 / 3.36 ( 840) hydrogen bonds : angle 3.49485 / 2.41 ( 2131) metal coordination : bond 0.00701 / 0.33 ( 8) metal coordination : angle 5.47874 / 2.41 ( 9) link_TRANS : bond 0.00126 / 0.07 ( 2) link_TRANS : angle 0.43158 / 0.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.411 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 59 GLU cc_start: 0.8764 (pm20) cc_final: 0.8364 (pm20) REVERT: C 205 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8306 (mm-30) REVERT: E 59 GLU cc_start: 0.8574 (pm20) cc_final: 0.8199 (pm20) REVERT: E 61 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8984 (mm) REVERT: E 94 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8450 (mm-30) REVERT: G -38 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8722 (mmmm) REVERT: H 34 LYS cc_start: 0.9258 (mtmm) cc_final: 0.8958 (mtmm) REVERT: H 86 ARG cc_start: 0.8257 (mmt90) cc_final: 0.7998 (mmt-90) REVERT: H 120 LYS cc_start: 0.9032 (ttpt) cc_final: 0.8449 (ttpt) REVERT: L 33 TRP cc_start: 0.8146 (m100) cc_final: 0.7298 (m100) REVERT: L 125 ARG cc_start: 0.8977 (mtm110) cc_final: 0.8636 (ptp-170) REVERT: L 136 ARG cc_start: 0.9452 (pmt-80) cc_final: 0.9176 (pmt-80) REVERT: L 147 MET cc_start: 0.8741 (mpp) cc_final: 0.8517 (mpp) outliers start: 21 outliers final: 20 residues processed: 194 average time/residue: 0.1377 time to fit residues: 37.8805 Evaluate side-chains 205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue -102 SER Chi-restraints excluded: chain G residue -95 SER Chi-restraints excluded: chain G residue -13 VAL Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 87 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 32 HIS L 46 GLN L 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.132825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.089692 restraints weight = 36532.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.088897 restraints weight = 26466.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.089833 restraints weight = 23709.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.090393 restraints weight = 18117.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.090636 restraints weight = 17596.256| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15482 Z= 0.152 Angle : 0.626 12.403 22186 Z= 0.346 Chirality : 0.041 0.232 2516 Planarity : 0.005 0.067 1794 Dihedral : 29.611 177.838 4413 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.71 % Allowed : 16.23 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.94 (0.27), residues: 1057 helix: 2.44 (0.21), residues: 646 sheet: -1.16 (0.81), residues: 33 loop : -0.54 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.017 0.001 TYR K 64 PHE 0.031 0.002 PHE L 50 TRP 0.027 0.003 TRP L 33 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (15472) covalent geometry : angle 0.61807 / 0.35 (22171) hydrogen bonds : bond 0.04959 / 3.29 ( 840) hydrogen bonds : angle 3.45987 / 2.39 ( 2131) metal coordination : bond 0.00694 / 0.34 ( 8) metal coordination : angle 5.10142 / 2.25 ( 9) link_TRANS : bond 0.00098 / 0.05 ( 2) link_TRANS : angle 0.40306 / 0.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.344 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 59 GLU cc_start: 0.8731 (pm20) cc_final: 0.8315 (pm20) REVERT: E 59 GLU cc_start: 0.8504 (pm20) cc_final: 0.8190 (pm20) REVERT: E 61 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8975 (mm) REVERT: E 94 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8438 (mm-30) REVERT: H 34 LYS cc_start: 0.9192 (mtmm) cc_final: 0.8915 (mtmm) REVERT: H 86 ARG cc_start: 0.8230 (mmt90) cc_final: 0.7960 (mmt-90) REVERT: H 120 LYS cc_start: 0.9037 (ttpt) cc_final: 0.8540 (ttpt) REVERT: K 42 SER cc_start: 0.7653 (p) cc_final: 0.7341 (p) REVERT: L 33 TRP cc_start: 0.7484 (m100) cc_final: 0.6967 (m100) outliers start: 25 outliers final: 18 residues processed: 197 average time/residue: 0.1367 time to fit residues: 38.5188 Evaluate side-chains 203 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue -102 SER Chi-restraints excluded: chain G residue -95 SER Chi-restraints excluded: chain G residue -13 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 112 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 114 optimal weight: 0.2980 chunk 42 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 86 optimal weight: 20.0000 chunk 66 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN L 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.133072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.080883 restraints weight = 49484.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.082329 restraints weight = 24945.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.082530 restraints weight = 16314.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.083268 restraints weight = 17013.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.083513 restraints weight = 15488.661| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15482 Z= 0.153 Angle : 0.648 13.032 22186 Z= 0.355 Chirality : 0.042 0.411 2516 Planarity : 0.005 0.057 1794 Dihedral : 29.621 177.774 4413 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.84 % Allowed : 17.42 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.88 (0.27), residues: 1057 helix: 2.39 (0.21), residues: 647 sheet: -1.32 (0.78), residues: 33 loop : -0.56 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 72 TYR 0.018 0.002 TYR B 88 PHE 0.032 0.002 PHE L 62 TRP 0.024 0.002 TRP L 33 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (15472) covalent geometry : angle 0.63985 / 0.35 (22171) hydrogen bonds : bond 0.04949 / 3.29 ( 840) hydrogen bonds : angle 3.42695 / 2.37 ( 2131) metal coordination : bond 0.00661 / 0.32 ( 8) metal coordination : angle 5.28995 / 2.32 ( 9) link_TRANS : bond 0.00092 / 0.05 ( 2) link_TRANS : angle 0.38299 / 0.19 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.434 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: symmetry clash REVERT: A 59 GLU cc_start: 0.8746 (pm20) cc_final: 0.8301 (pm20) REVERT: E 59 GLU cc_start: 0.8550 (pm20) cc_final: 0.8224 (pm20) REVERT: E 94 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8443 (mm-30) REVERT: H 34 LYS cc_start: 0.9257 (mtmm) cc_final: 0.8950 (mtmm) REVERT: H 86 ARG cc_start: 0.8247 (mmt90) cc_final: 0.7999 (mmt-90) REVERT: H 120 LYS cc_start: 0.9023 (ttpt) cc_final: 0.8446 (ttpt) REVERT: L 33 TRP cc_start: 0.8028 (m100) cc_final: 0.7320 (m100) outliers start: 17 outliers final: 17 residues processed: 189 average time/residue: 0.1292 time to fit residues: 35.0977 Evaluate side-chains 200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 231 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue -102 SER Chi-restraints excluded: chain G residue -95 SER Chi-restraints excluded: chain G residue -13 VAL Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 23 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 87 optimal weight: 20.0000 chunk 123 optimal weight: 50.0000 chunk 127 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 32 HIS L 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.132843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.080437 restraints weight = 42978.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.081615 restraints weight = 22902.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.082266 restraints weight = 17078.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.082422 restraints weight = 15193.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.082658 restraints weight = 14471.629| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15482 Z= 0.159 Angle : 0.641 13.280 22186 Z= 0.353 Chirality : 0.042 0.339 2516 Planarity : 0.005 0.053 1794 Dihedral : 29.651 177.723 4413 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.16 % Allowed : 17.53 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.86 (0.26), residues: 1057 helix: 2.38 (0.21), residues: 647 sheet: -1.41 (0.74), residues: 33 loop : -0.57 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 5 TYR 0.016 0.001 TYR K 64 PHE 0.035 0.002 PHE L 62 TRP 0.023 0.002 TRP L 33 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (15472) covalent geometry : angle 0.63161 / 0.35 (22171) hydrogen bonds : bond 0.05012 / 3.34 ( 840) hydrogen bonds : angle 3.46287 / 2.40 ( 2131) metal coordination : bond 0.00688 / 0.33 ( 8) metal coordination : angle 5.42738 / 2.38 ( 9) link_TRANS : bond 0.00107 / 0.06 ( 2) link_TRANS : angle 0.38504 / 0.19 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2622.45 seconds wall clock time: 45 minutes 51.37 seconds (2751.37 seconds total)