Starting phenix.real_space_refine on Fri Jul 3 15:53:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7i_38099/07_2026/8x7i_38099.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7i_38099/07_2026/8x7i_38099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x7i_38099/07_2026/8x7i_38099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7i_38099/07_2026/8x7i_38099.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7i_38099/07_2026/8x7i_38099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7i_38099/07_2026/8x7i_38099.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1119 atoms to isotropic. 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 28 5.16 5 C 8076 2.51 5 N 2655 2.21 5 O 3245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 14300 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 845 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "K" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1125 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "L" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 641 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 73} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 413 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 56} Chain breaks: 3 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "L" 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 13447 SG CYS L 31 56.643 71.877 28.876 1.00218.04 S ATOM 13589 SG CYS L 51 58.205 75.289 28.905 1.00210.14 S ATOM 13613 SG CYS L 54 54.564 75.086 28.068 1.00213.50 S ATOM 13338 SG CYS L 16 67.989 71.834 23.293 1.00283.03 S ATOM 13356 SG CYS L 19 71.632 71.909 22.328 1.00282.47 S ATOM 13486 SG CYS L 36 70.625 69.933 25.344 1.00253.66 S ATOM 13504 SG CYS L 39 70.429 73.629 25.607 1.00248.31 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 75 " occ=0.45 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.45 Time building chain proxies: 2.59, per 1000 atoms: 0.18 Number of scatterers: 14300 At special positions: 0 Unit cell: (118.14, 128.88, 112.77, 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 28 16.00 P 294 15.00 O 3245 8.00 N 2655 7.00 C 8076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 331.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 33 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 54 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 16 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 19 " Number of angles added : 9 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2002 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 13 sheets defined 62.3% alpha, 4.2% beta 143 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.594A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.816A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.399A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.627A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 29 removed outlier: 3.667A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.548A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.523A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.514A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.587A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.512A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.548A pdb=" N THR H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 2 through 16 Processing helix chain 'K' and resid 86 through 91 Processing helix chain 'K' and resid 98 through 112 Processing helix chain 'K' and resid 120 through 130 Processing helix chain 'K' and resid 130 through 145 Processing helix chain 'L' and resid 10 through 15 Processing helix chain 'L' and resid 36 through 47 removed outlier: 4.833A pdb=" N GLU L 45 " --> pdb=" O GLN L 41 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA L 47 " --> pdb=" O THR L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 69 removed outlier: 3.757A pdb=" N ARG L 67 " --> pdb=" O ARG L 63 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG L 68 " --> pdb=" O TYR L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 84 Processing helix chain 'M' and resid 22 through 35 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.869A 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 42 through 43 removed outlier: 7.469A pdb=" N ARG C 42 " --> 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 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.817A pdb=" N THR C 101 " --> 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: 7.062A 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 42 through 43 removed outlier: 7.292A pdb=" N ARG G 42 " --> 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 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 32 through 38 Processing sheet with id=AB3, first strand: chain 'L' and resid 27 through 28 removed outlier: 3.552A pdb=" N LEU L 35 " --> pdb=" O VAL L 27 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 3 through 6 484 hydrogen bonds defined for protein. 1431 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 343 hydrogen bonds 598 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3279 1.33 - 1.45: 4408 1.45 - 1.57: 6848 1.57 - 1.69: 586 1.69 - 1.81: 44 Bond restraints: 15165 Sorted by residual: bond pdb=" C3' DA J -67 " pdb=" C2' DA J -67 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DG I 4 " pdb=" O3' DG I 4 " ideal model delta sigma weight residual 1.435 1.395 0.040 1.30e-02 5.92e+03 9.57e+00 bond pdb=" C3' DC I 61 " pdb=" C2' DC I 61 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.97e+00 bond pdb=" C3' DG I 10 " pdb=" C2' DG I 10 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.86e+00 bond pdb=" C3' DG I 0 " pdb=" C2' DG I 0 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.44e+00 ... (remaining 15160 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 20325 1.44 - 2.88: 1362 2.88 - 4.32: 78 4.32 - 5.76: 15 5.76 - 7.20: 1 Bond angle restraints: 21781 Sorted by residual: angle pdb=" O4' DC I -26 " pdb=" C4' DC I -26 " pdb=" C3' DC I -26 " ideal model delta sigma weight residual 106.00 103.18 2.82 6.00e-01 2.78e+00 2.21e+01 angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" N3 DT I -24 " pdb=" C4 DT I -24 " pdb=" O4 DT I -24 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.99e+01 angle pdb=" O4' DA J 32 " pdb=" C4' DA J 32 " pdb=" C3' DA J 32 " ideal model delta sigma weight residual 106.00 103.33 2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT J 71 " pdb=" C4 DT J 71 " pdb=" O4 DT J 71 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 ... (remaining 21776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 7056 35.16 - 70.32: 1302 70.32 - 105.48: 11 105.48 - 140.64: 1 140.64 - 175.80: 2 Dihedral angle restraints: 8372 sinusoidal: 5285 harmonic: 3087 Sorted by residual: dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 44.20 175.80 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 58.69 161.31 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 84.74 135.26 1 3.50e+01 8.16e-04 1.34e+01 ... (remaining 8369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1633 0.040 - 0.080: 589 0.080 - 0.120: 207 0.120 - 0.160: 57 0.160 - 0.200: 3 Chirality restraints: 2489 Sorted by residual: chirality pdb=" C3' DT I -59 " pdb=" C4' DT I -59 " pdb=" O3' DT I -59 " pdb=" C2' DT I -59 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" C3' DT I 33 " pdb=" C4' DT I 33 " pdb=" O3' DT I 33 " pdb=" C2' DT I 33 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" C3' DT J -39 " pdb=" C4' DT J -39 " pdb=" O3' DT J -39 " pdb=" C2' DT J -39 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.46e-01 ... (remaining 2486 not shown) Planarity restraints: 1746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU L 3 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO L 4 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO L 4 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 4 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " 0.024 2.00e-02 2.50e+03 9.90e-03 2.69e+00 pdb=" N9 DA I 47 " -0.017 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " -0.007 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " -0.024 2.00e-02 2.50e+03 9.41e-03 2.66e+00 pdb=" N9 DG I -35 " 0.019 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" O6 DG I -35 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " 0.003 2.00e-02 2.50e+03 ... (remaining 1743 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 425 2.65 - 3.22: 12761 3.22 - 3.78: 27171 3.78 - 4.34: 34185 4.34 - 4.90: 49782 Nonbonded interactions: 124324 Sorted by model distance: nonbonded pdb=" N2 DG I 51 " pdb=" O2 DC J -51 " model vdw 2.093 2.496 nonbonded pdb=" N2 DG I 46 " pdb=" O2 DC J -46 " model vdw 2.094 2.496 nonbonded pdb=" O2 DC I 52 " pdb=" N2 DG J -52 " model vdw 2.109 2.496 nonbonded pdb=" O2 DC I 40 " pdb=" N2 DG J -40 " model vdw 2.115 2.496 nonbonded pdb=" O2 DC I -52 " pdb=" N2 DG J 52 " model vdw 2.122 2.496 ... (remaining 124319 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 19 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 10 through 14 or resid 16 through 118)) selection = (chain 'G' and (resid 10 through 14 or resid 16 through 118)) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.880 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 15173 Z= 0.563 Angle : 0.734 7.198 21790 Z= 0.625 Chirality : 0.048 0.200 2489 Planarity : 0.004 0.053 1746 Dihedral : 25.488 175.796 6370 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.87 % Favored : 96.03 % Rotamer: Outliers : 1.85 % Allowed : 4.61 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % 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: 1.53 (0.27), residues: 1033 helix: 1.99 (0.21), residues: 656 sheet: -0.84 (1.01), residues: 24 loop : -0.72 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 88 TYR 0.008 0.001 TYR B 51 PHE 0.011 0.001 PHE E 67 TRP 0.010 0.002 TRP K 93 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.56 (15165) covalent geometry : angle 0.73181 / 0.62 (21781) hydrogen bonds : bond 0.13883 / 9.23 ( 827) hydrogen bonds : angle 4.47578 / 3.22 ( 2029) metal coordination : bond 0.00525 / 0.21 ( 8) metal coordination : angle 2.98548 / 1.60 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 273 time to evaluate : 0.358 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: symmetry clash REVERT: A 73 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8664 (tm-30) REVERT: C 38 ASN cc_start: 0.8754 (m-40) cc_final: 0.7563 (m-40) REVERT: C 68 ASN cc_start: 0.8990 (m-40) cc_final: 0.8672 (m-40) REVERT: E 73 GLU cc_start: 0.8063 (tt0) cc_final: 0.7672 (tt0) REVERT: E 94 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8308 (mm-30) REVERT: E 115 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8944 (mppt) REVERT: F 88 TYR cc_start: 0.8862 (m-10) cc_final: 0.6969 (m-10) REVERT: F 91 LYS cc_start: 0.9298 (ttmt) cc_final: 0.8971 (ttpt) REVERT: G 61 GLU cc_start: 0.8624 (tp30) cc_final: 0.8342 (mm-30) REVERT: D 93 GLU cc_start: 0.8250 (mp0) cc_final: 0.7960 (mp0) REVERT: D 116 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8617 (mtpt) REVERT: H 68 ASP cc_start: 0.8790 (t70) cc_final: 0.8487 (t0) REVERT: H 72 ARG cc_start: 0.9054 (mtt180) cc_final: 0.8848 (mtt180) REVERT: K 38 MET cc_start: 0.8957 (mtt) cc_final: 0.8534 (tpt) REVERT: K 62 PHE cc_start: 0.9102 (m-80) cc_final: 0.8871 (m-80) REVERT: K 87 ASP cc_start: 0.8780 (p0) cc_final: 0.8481 (p0) REVERT: K 92 GLN cc_start: 0.8971 (tp-100) cc_final: 0.8579 (tp-100) REVERT: K 120 VAL cc_start: 0.7361 (t) cc_final: 0.7125 (t) REVERT: L 20 MET cc_start: 0.7447 (mmt) cc_final: 0.7150 (mmt) REVERT: L 45 GLU cc_start: 0.8965 (pm20) cc_final: 0.8601 (pm20) REVERT: L 60 SER cc_start: 0.8715 (m) cc_final: 0.8424 (m) REVERT: L 73 ASN cc_start: 0.7355 (OUTLIER) cc_final: 0.7141 (t0) outliers start: 16 outliers final: 5 residues processed: 285 average time/residue: 0.1587 time to fit residues: 60.8744 Evaluate side-chains 207 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain L residue 14 CYS Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 40.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 30.0000 chunk 35 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN E 68 GLN E 76 GLN F 27 GLN G 38 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN D 95 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS L 41 GLN L 73 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.049119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.032780 restraints weight = 81352.344| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 3.00 r_work: 0.2541 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2532 r_free = 0.2532 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15173 Z= 0.216 Angle : 0.688 9.862 21790 Z= 0.400 Chirality : 0.045 0.301 2489 Planarity : 0.005 0.055 1746 Dihedral : 29.717 176.262 4396 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.32 % Rotamer: Outliers : 3.00 % Allowed : 13.38 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % 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: 1.61 (0.27), residues: 1033 helix: 2.04 (0.21), residues: 662 sheet: -0.54 (1.12), residues: 18 loop : -0.75 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 35 TYR 0.024 0.002 TYR H 83 PHE 0.014 0.002 PHE K 51 TRP 0.025 0.003 TRP K 141 HIS 0.004 0.001 HIS L 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.22 (15165) covalent geometry : angle 0.68560 / 0.40 (21781) hydrogen bonds : bond 0.09933 / 6.75 ( 827) hydrogen bonds : angle 3.79551 / 2.76 ( 2029) metal coordination : bond 0.00823 / 0.36 ( 8) metal coordination : angle 2.64250 / 1.41 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 0.382 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: symmetry clash REVERT: A 59 GLU cc_start: 0.9053 (pm20) cc_final: 0.8791 (pm20) REVERT: A 73 GLU cc_start: 0.9465 (tm-30) cc_final: 0.9231 (tm-30) REVERT: A 94 GLU cc_start: 0.8941 (tp30) cc_final: 0.8735 (tp30) REVERT: B 88 TYR cc_start: 0.9201 (m-10) cc_final: 0.8832 (m-80) REVERT: C 24 GLN cc_start: 0.9384 (mm-40) cc_final: 0.8819 (mp10) REVERT: C 56 GLU cc_start: 0.9285 (tt0) cc_final: 0.8776 (tt0) REVERT: C 68 ASN cc_start: 0.9103 (m-40) cc_final: 0.8703 (m-40) REVERT: E 94 GLU cc_start: 0.9234 (mm-30) cc_final: 0.9024 (mm-30) REVERT: E 115 LYS cc_start: 0.9450 (OUTLIER) cc_final: 0.9246 (mppt) REVERT: F 91 LYS cc_start: 0.9427 (ttmt) cc_final: 0.9082 (ttpt) REVERT: G 61 GLU cc_start: 0.9105 (tp30) cc_final: 0.8865 (tp30) REVERT: D 93 GLU cc_start: 0.8891 (mp0) cc_final: 0.8582 (mp0) REVERT: D 116 LYS cc_start: 0.9467 (OUTLIER) cc_final: 0.9124 (mtpt) REVERT: H 33 ARG cc_start: 0.8442 (mtp85) cc_final: 0.7573 (ttt180) REVERT: H 68 ASP cc_start: 0.9262 (t70) cc_final: 0.9017 (t0) REVERT: H 85 LYS cc_start: 0.9474 (mmtt) cc_final: 0.9125 (mmmt) REVERT: K 1 MET cc_start: 0.7495 (tmm) cc_final: 0.7122 (tmm) REVERT: K 16 ASP cc_start: 0.9288 (m-30) cc_final: 0.9015 (p0) REVERT: K 38 MET cc_start: 0.9083 (mtt) cc_final: 0.8690 (tpt) REVERT: K 69 PHE cc_start: 0.8718 (m-80) cc_final: 0.8431 (t80) REVERT: K 87 ASP cc_start: 0.8982 (p0) cc_final: 0.8739 (p0) REVERT: K 92 GLN cc_start: 0.9005 (tp-100) cc_final: 0.8641 (tp-100) REVERT: K 120 VAL cc_start: 0.7504 (t) cc_final: 0.7224 (t) REVERT: L 20 MET cc_start: 0.7490 (mmt) cc_final: 0.7131 (mmt) outliers start: 26 outliers final: 16 residues processed: 235 average time/residue: 0.1170 time to fit residues: 38.5596 Evaluate side-chains 224 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 45 TYR Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain L residue 40 PHE Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.7980 chunk 77 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 102 optimal weight: 0.3980 chunk 98 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN D 95 GLN ** H 84 ASN ** 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 = 0.3391 r_free = 0.3391 target = 0.049651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.033234 restraints weight = 81309.583| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.01 r_work: 0.2563 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15173 Z= 0.148 Angle : 0.624 10.337 21790 Z= 0.370 Chirality : 0.043 0.272 2489 Planarity : 0.004 0.056 1746 Dihedral : 29.685 174.403 4393 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.81 % Favored : 97.10 % Rotamer: Outliers : 2.19 % Allowed : 15.69 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % 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: 1.70 (0.27), residues: 1033 helix: 2.20 (0.21), residues: 656 sheet: -1.18 (0.87), residues: 24 loop : -0.79 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 125 TYR 0.026 0.002 TYR D 83 PHE 0.014 0.002 PHE K 56 TRP 0.014 0.002 TRP K 141 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.15 (15165) covalent geometry : angle 0.62241 / 0.37 (21781) hydrogen bonds : bond 0.09123 / 6.17 ( 827) hydrogen bonds : angle 3.44620 / 2.51 ( 2029) metal coordination : bond 0.00428 / 0.18 ( 8) metal coordination : angle 2.47973 / 1.29 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 228 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9161 (pm20) cc_final: 0.8831 (pm20) REVERT: A 73 GLU cc_start: 0.9468 (tm-30) cc_final: 0.9106 (tt0) REVERT: A 94 GLU cc_start: 0.8917 (tp30) cc_final: 0.8605 (tt0) REVERT: A 125 GLN cc_start: 0.9293 (mt0) cc_final: 0.8229 (mt0) REVERT: B 88 TYR cc_start: 0.9174 (m-10) cc_final: 0.8556 (m-80) REVERT: C 24 GLN cc_start: 0.9283 (mm-40) cc_final: 0.8812 (mp10) REVERT: E 94 GLU cc_start: 0.9263 (mm-30) cc_final: 0.9011 (mm-30) REVERT: F 91 LYS cc_start: 0.9428 (ttmt) cc_final: 0.9080 (ttpt) REVERT: G 61 GLU cc_start: 0.9062 (tp30) cc_final: 0.8766 (tp30) REVERT: D 83 TYR cc_start: 0.8331 (m-10) cc_final: 0.8110 (m-80) REVERT: D 93 GLU cc_start: 0.8897 (mp0) cc_final: 0.8573 (mp0) REVERT: H 33 ARG cc_start: 0.8404 (mtp85) cc_final: 0.7775 (ttt180) REVERT: H 105 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7771 (tm-30) REVERT: H 106 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9130 (mt) REVERT: H 113 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8934 (mm-30) REVERT: K 1 MET cc_start: 0.7489 (tmm) cc_final: 0.7174 (tmm) REVERT: K 38 MET cc_start: 0.9024 (mtt) cc_final: 0.8697 (tpt) REVERT: K 87 ASP cc_start: 0.9049 (p0) cc_final: 0.8822 (p0) REVERT: K 92 GLN cc_start: 0.9110 (tp-100) cc_final: 0.8759 (tp-100) REVERT: K 120 VAL cc_start: 0.7625 (t) cc_final: 0.7074 (m) REVERT: K 125 ARG cc_start: 0.8894 (mtm110) cc_final: 0.8584 (ptp-170) REVERT: K 147 MET cc_start: 0.8673 (mtt) cc_final: 0.8262 (mpp) REVERT: L 20 MET cc_start: 0.7513 (mmt) cc_final: 0.7135 (mmt) REVERT: L 45 GLU cc_start: 0.9336 (pm20) cc_final: 0.9091 (pm20) outliers start: 19 outliers final: 13 residues processed: 236 average time/residue: 0.1226 time to fit residues: 40.5384 Evaluate side-chains 216 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 40 PHE Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 55 optimal weight: 30.0000 chunk 117 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 69 optimal weight: 30.0000 chunk 112 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 18 optimal weight: 0.6980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS G 38 ASN L 41 GLN L 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.049092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.032654 restraints weight = 81620.482| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.98 r_work: 0.2542 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15173 Z= 0.202 Angle : 0.647 10.392 21790 Z= 0.376 Chirality : 0.043 0.263 2489 Planarity : 0.004 0.057 1746 Dihedral : 29.816 174.087 4381 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.77 % Allowed : 15.80 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % 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: 1.75 (0.27), residues: 1033 helix: 2.25 (0.21), residues: 650 sheet: -1.01 (0.89), residues: 24 loop : -0.76 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 5 TYR 0.021 0.002 TYR K 145 PHE 0.012 0.002 PHE E 67 TRP 0.018 0.003 TRP K 141 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.20 (15165) covalent geometry : angle 0.64551 / 0.38 (21781) hydrogen bonds : bond 0.08937 / 6.06 ( 827) hydrogen bonds : angle 3.51458 / 2.58 ( 2029) metal coordination : bond 0.00528 / 0.23 ( 8) metal coordination : angle 2.51695 / 1.36 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9100 (pm20) cc_final: 0.8750 (pm20) REVERT: A 73 GLU cc_start: 0.9446 (tm-30) cc_final: 0.9200 (tm-30) REVERT: A 94 GLU cc_start: 0.8888 (tp30) cc_final: 0.8593 (tt0) REVERT: A 125 GLN cc_start: 0.9206 (mt0) cc_final: 0.8958 (mt0) REVERT: B 88 TYR cc_start: 0.9176 (m-10) cc_final: 0.8619 (m-80) REVERT: C 24 GLN cc_start: 0.9344 (mm-40) cc_final: 0.8838 (mp10) REVERT: C 56 GLU cc_start: 0.9300 (tt0) cc_final: 0.8800 (tt0) REVERT: E 94 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8951 (mm-30) REVERT: F 91 LYS cc_start: 0.9430 (ttmt) cc_final: 0.9110 (ttpt) REVERT: G 61 GLU cc_start: 0.9086 (tp30) cc_final: 0.8774 (tp30) REVERT: G 64 GLU cc_start: 0.9232 (OUTLIER) cc_final: 0.8796 (pp20) REVERT: D 83 TYR cc_start: 0.8262 (m-10) cc_final: 0.7945 (m-10) REVERT: D 93 GLU cc_start: 0.8884 (mp0) cc_final: 0.8611 (mp0) REVERT: H 33 ARG cc_start: 0.8400 (mtp85) cc_final: 0.7673 (ttt180) REVERT: H 83 TYR cc_start: 0.8550 (m-10) cc_final: 0.8150 (m-10) REVERT: H 105 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7748 (tm-30) REVERT: H 106 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9131 (mt) REVERT: H 113 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8949 (mm-30) REVERT: K 1 MET cc_start: 0.7508 (tmm) cc_final: 0.7162 (tmm) REVERT: K 38 MET cc_start: 0.9061 (mtt) cc_final: 0.8695 (tpt) REVERT: K 87 ASP cc_start: 0.9034 (p0) cc_final: 0.8808 (p0) REVERT: K 92 GLN cc_start: 0.9095 (tp-100) cc_final: 0.8787 (tp-100) REVERT: K 120 VAL cc_start: 0.7563 (OUTLIER) cc_final: 0.7024 (t) REVERT: K 147 MET cc_start: 0.8745 (mtt) cc_final: 0.8240 (mpp) REVERT: L 20 MET cc_start: 0.7519 (mmt) cc_final: 0.7166 (mmt) REVERT: L 50 CYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7210 (t) REVERT: L 73 ASN cc_start: 0.7420 (t0) cc_final: 0.7174 (t0) outliers start: 24 outliers final: 16 residues processed: 218 average time/residue: 0.1159 time to fit residues: 36.1503 Evaluate side-chains 215 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain L residue 40 PHE Chi-restraints excluded: chain L residue 50 CYS Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 20.0000 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.050049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.033673 restraints weight = 79529.416| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.96 r_work: 0.2574 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15173 Z= 0.142 Angle : 0.622 10.281 21790 Z= 0.365 Chirality : 0.042 0.265 2489 Planarity : 0.004 0.059 1746 Dihedral : 29.795 173.735 4381 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.00 % Allowed : 16.49 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % 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: 1.76 (0.27), residues: 1033 helix: 2.26 (0.21), residues: 649 sheet: -0.83 (0.88), residues: 24 loop : -0.76 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 5 TYR 0.016 0.001 TYR H 121 PHE 0.012 0.001 PHE A 67 TRP 0.015 0.002 TRP K 141 HIS 0.004 0.001 HIS K 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (15165) covalent geometry : angle 0.61997 / 0.37 (21781) hydrogen bonds : bond 0.08896 / 6.02 ( 827) hydrogen bonds : angle 3.34561 / 2.45 ( 2029) metal coordination : bond 0.00438 / 0.18 ( 8) metal coordination : angle 2.51392 / 1.34 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9073 (pm20) cc_final: 0.8736 (pm20) REVERT: A 73 GLU cc_start: 0.9448 (tm-30) cc_final: 0.9184 (tm-30) REVERT: A 94 GLU cc_start: 0.8875 (tp30) cc_final: 0.8563 (tt0) REVERT: B 88 TYR cc_start: 0.9135 (m-10) cc_final: 0.8371 (m-80) REVERT: C 24 GLN cc_start: 0.9275 (mm-40) cc_final: 0.8802 (mp10) REVERT: C 56 GLU cc_start: 0.9275 (tt0) cc_final: 0.8842 (tt0) REVERT: E 73 GLU cc_start: 0.8693 (tt0) cc_final: 0.8486 (tt0) REVERT: F 91 LYS cc_start: 0.9429 (ttmt) cc_final: 0.9118 (ttpt) REVERT: G 61 GLU cc_start: 0.9040 (tp30) cc_final: 0.8774 (tp30) REVERT: G 64 GLU cc_start: 0.9293 (OUTLIER) cc_final: 0.8891 (pp20) REVERT: D 83 TYR cc_start: 0.8233 (m-10) cc_final: 0.7829 (m-10) REVERT: D 93 GLU cc_start: 0.8849 (mp0) cc_final: 0.8598 (mp0) REVERT: H 33 ARG cc_start: 0.8332 (mtp85) cc_final: 0.7571 (ttt180) REVERT: H 83 TYR cc_start: 0.8561 (m-10) cc_final: 0.8213 (m-10) REVERT: H 105 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7733 (tm-30) REVERT: H 106 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9115 (mt) REVERT: H 113 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8931 (mm-30) REVERT: K 1 MET cc_start: 0.7494 (tmm) cc_final: 0.7166 (tmm) REVERT: K 38 MET cc_start: 0.9102 (mtt) cc_final: 0.8778 (tpt) REVERT: K 87 ASP cc_start: 0.9028 (p0) cc_final: 0.8820 (p0) REVERT: K 92 GLN cc_start: 0.9065 (tp-100) cc_final: 0.8800 (tp-100) REVERT: K 120 VAL cc_start: 0.7714 (t) cc_final: 0.7497 (t) REVERT: K 147 MET cc_start: 0.8641 (mtt) cc_final: 0.8150 (mpp) REVERT: L 20 MET cc_start: 0.7501 (mmt) cc_final: 0.7243 (mmt) REVERT: L 73 ASN cc_start: 0.7332 (t0) cc_final: 0.7055 (m110) outliers start: 26 outliers final: 16 residues processed: 218 average time/residue: 0.1122 time to fit residues: 35.0672 Evaluate side-chains 220 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 45 TYR Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain L residue 40 PHE Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 36 optimal weight: 0.0020 chunk 80 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 26 optimal weight: 0.0570 chunk 40 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.5106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN G 38 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 ASN L 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.050442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.034113 restraints weight = 79646.953| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 2.96 r_work: 0.2591 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15173 Z= 0.138 Angle : 0.620 8.943 21790 Z= 0.363 Chirality : 0.042 0.258 2489 Planarity : 0.004 0.060 1746 Dihedral : 29.754 173.049 4381 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.11 % Allowed : 16.15 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % 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: 1.87 (0.27), residues: 1033 helix: 2.34 (0.20), residues: 649 sheet: -0.74 (0.86), residues: 29 loop : -0.71 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 136 TYR 0.018 0.001 TYR L 64 PHE 0.013 0.001 PHE K 62 TRP 0.011 0.001 TRP K 141 HIS 0.003 0.001 HIS K 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.14 (15165) covalent geometry : angle 0.61817 / 0.36 (21781) hydrogen bonds : bond 0.08848 / 5.99 ( 827) hydrogen bonds : angle 3.24247 / 2.38 ( 2029) metal coordination : bond 0.00638 / 0.29 ( 8) metal coordination : angle 2.29566 / 1.03 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.290 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: 0.9080 (pm20) cc_final: 0.8746 (pm20) REVERT: A 62 ILE cc_start: 0.9444 (mt) cc_final: 0.9113 (mt) REVERT: A 73 GLU cc_start: 0.9443 (tm-30) cc_final: 0.9114 (tt0) REVERT: A 94 GLU cc_start: 0.8817 (tp30) cc_final: 0.8561 (tt0) REVERT: A 97 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8496 (mm-30) REVERT: B 23 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8276 (ptp90) REVERT: B 62 LEU cc_start: 0.9791 (mt) cc_final: 0.9570 (mt) REVERT: C 13 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7680 (pmtt) REVERT: C 24 GLN cc_start: 0.9217 (mm-40) cc_final: 0.8780 (mp10) REVERT: C 56 GLU cc_start: 0.9275 (tt0) cc_final: 0.8892 (tt0) REVERT: E 73 GLU cc_start: 0.8725 (tt0) cc_final: 0.8494 (tt0) REVERT: F 91 LYS cc_start: 0.9426 (ttmt) cc_final: 0.9109 (ttpt) REVERT: G 61 GLU cc_start: 0.8985 (tp30) cc_final: 0.8753 (tp30) REVERT: G 64 GLU cc_start: 0.9320 (OUTLIER) cc_final: 0.9033 (pp20) REVERT: D 93 GLU cc_start: 0.8828 (mp0) cc_final: 0.8610 (mp0) REVERT: H 33 ARG cc_start: 0.8362 (mtp85) cc_final: 0.7656 (ttt90) REVERT: H 83 TYR cc_start: 0.8536 (m-10) cc_final: 0.8186 (m-10) REVERT: H 105 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7742 (tm-30) REVERT: H 106 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9105 (mt) REVERT: H 113 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8885 (mt-10) REVERT: K 1 MET cc_start: 0.7564 (tmm) cc_final: 0.7229 (tmm) REVERT: K 38 MET cc_start: 0.9088 (mtt) cc_final: 0.8778 (tpt) REVERT: K 92 GLN cc_start: 0.8985 (tp-100) cc_final: 0.8761 (tp-100) REVERT: K 120 VAL cc_start: 0.7667 (OUTLIER) cc_final: 0.7424 (t) REVERT: K 136 ARG cc_start: 0.9304 (ppt170) cc_final: 0.8893 (ttp-110) REVERT: K 147 MET cc_start: 0.8568 (mtt) cc_final: 0.8080 (mpp) REVERT: L 20 MET cc_start: 0.7241 (mmt) cc_final: 0.6853 (mmt) REVERT: L 50 CYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7514 (t) REVERT: L 73 ASN cc_start: 0.7362 (t0) cc_final: 0.7134 (m110) outliers start: 27 outliers final: 12 residues processed: 227 average time/residue: 0.1165 time to fit residues: 37.8637 Evaluate side-chains 222 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 45 TYR Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain L residue 40 PHE Chi-restraints excluded: chain L residue 50 CYS Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 71 optimal weight: 20.0000 chunk 26 optimal weight: 0.2980 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 43 optimal weight: 0.1980 chunk 46 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 103 optimal weight: 30.0000 chunk 79 optimal weight: 20.0000 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 68 ASN ** G 38 ASN ** 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 = 0.3383 r_free = 0.3383 target = 0.049502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.033146 restraints weight = 81627.013| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.96 r_work: 0.2563 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15173 Z= 0.174 Angle : 0.638 9.078 21790 Z= 0.367 Chirality : 0.042 0.249 2489 Planarity : 0.004 0.059 1746 Dihedral : 29.899 173.581 4381 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.31 % Allowed : 16.96 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.27), residues: 1033 helix: 2.43 (0.20), residues: 649 sheet: -0.73 (0.84), residues: 29 loop : -0.57 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 136 TYR 0.020 0.002 TYR B 88 PHE 0.012 0.001 PHE E 67 TRP 0.007 0.001 TRP K 141 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (15165) covalent geometry : angle 0.63449 / 0.37 (21781) hydrogen bonds : bond 0.08576 / 5.82 ( 827) hydrogen bonds : angle 3.34092 / 2.46 ( 2029) metal coordination : bond 0.00914 / 0.42 ( 8) metal coordination : angle 3.23239 / 1.66 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9107 (pm20) cc_final: 0.8770 (pm20) REVERT: A 73 GLU cc_start: 0.9433 (tm-30) cc_final: 0.9156 (tm-30) REVERT: A 94 GLU cc_start: 0.8856 (tp30) cc_final: 0.8595 (tt0) REVERT: B 23 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8122 (ptp90) REVERT: C 13 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7698 (pmtt) REVERT: C 24 GLN cc_start: 0.9330 (mm-40) cc_final: 0.8807 (mp10) REVERT: C 56 GLU cc_start: 0.9329 (tt0) cc_final: 0.8906 (tt0) REVERT: E 73 GLU cc_start: 0.8752 (tt0) cc_final: 0.8527 (tt0) REVERT: F 91 LYS cc_start: 0.9434 (ttmt) cc_final: 0.9118 (ttpt) REVERT: G 61 GLU cc_start: 0.9020 (tp30) cc_final: 0.8776 (tp30) REVERT: G 64 GLU cc_start: 0.9330 (OUTLIER) cc_final: 0.9049 (pp20) REVERT: D 93 GLU cc_start: 0.8901 (mp0) cc_final: 0.8675 (mp0) REVERT: H 33 ARG cc_start: 0.8447 (mtp85) cc_final: 0.7727 (ttt90) REVERT: H 83 TYR cc_start: 0.8563 (m-10) cc_final: 0.8224 (m-10) REVERT: H 105 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7695 (tm-30) REVERT: H 106 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9141 (mt) REVERT: H 113 GLU cc_start: 0.9307 (mm-30) cc_final: 0.8890 (mt-10) REVERT: K 1 MET cc_start: 0.7473 (tmm) cc_final: 0.7138 (tmm) REVERT: K 38 MET cc_start: 0.9066 (mtt) cc_final: 0.8799 (tpt) REVERT: K 87 ASP cc_start: 0.8848 (p0) cc_final: 0.8639 (t0) REVERT: K 120 VAL cc_start: 0.7602 (OUTLIER) cc_final: 0.7351 (t) REVERT: K 136 ARG cc_start: 0.9329 (ppt170) cc_final: 0.9021 (tmm-80) REVERT: L 20 MET cc_start: 0.7181 (mmt) cc_final: 0.6799 (mmt) REVERT: L 50 CYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7607 (t) REVERT: L 73 ASN cc_start: 0.7432 (t0) cc_final: 0.7187 (m-40) outliers start: 20 outliers final: 11 residues processed: 217 average time/residue: 0.1305 time to fit residues: 40.3114 Evaluate side-chains 214 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 45 TYR Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain L residue 50 CYS Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 36 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 27 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 81 optimal weight: 20.0000 chunk 3 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 68 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 GLN K 143 GLN L 41 GLN L 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.050231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.033940 restraints weight = 81428.038| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.99 r_work: 0.2590 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15173 Z= 0.140 Angle : 0.638 13.420 21790 Z= 0.367 Chirality : 0.042 0.256 2489 Planarity : 0.004 0.061 1746 Dihedral : 29.855 173.359 4381 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.31 % Allowed : 17.19 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.27), residues: 1033 helix: 2.45 (0.20), residues: 647 sheet: -0.53 (0.93), residues: 24 loop : -0.60 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 99 TYR 0.039 0.002 TYR D 83 PHE 0.011 0.001 PHE E 67 TRP 0.032 0.003 TRP K 141 HIS 0.007 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (15165) covalent geometry : angle 0.63528 / 0.37 (21781) hydrogen bonds : bond 0.08661 / 5.86 ( 827) hydrogen bonds : angle 3.25182 / 2.38 ( 2029) metal coordination : bond 0.00668 / 0.30 ( 8) metal coordination : angle 2.95036 / 1.51 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9102 (pm20) cc_final: 0.8768 (pm20) REVERT: A 73 GLU cc_start: 0.9437 (tm-30) cc_final: 0.9162 (tm-30) REVERT: A 79 LYS cc_start: 0.9138 (tptm) cc_final: 0.8603 (tptp) REVERT: A 94 GLU cc_start: 0.8821 (tp30) cc_final: 0.8584 (tt0) REVERT: B 62 LEU cc_start: 0.9787 (mt) cc_final: 0.9570 (mt) REVERT: B 88 TYR cc_start: 0.8859 (m-80) cc_final: 0.8519 (m-80) REVERT: C 13 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7717 (pmtt) REVERT: C 24 GLN cc_start: 0.9263 (mm-40) cc_final: 0.8811 (mp10) REVERT: C 56 GLU cc_start: 0.9284 (tt0) cc_final: 0.8928 (tt0) REVERT: E 73 GLU cc_start: 0.8704 (tt0) cc_final: 0.8460 (tt0) REVERT: F 91 LYS cc_start: 0.9435 (ttmt) cc_final: 0.9120 (ttpt) REVERT: G 61 GLU cc_start: 0.8990 (tp30) cc_final: 0.8757 (tp30) REVERT: G 64 GLU cc_start: 0.9329 (OUTLIER) cc_final: 0.9039 (pp20) REVERT: H 33 ARG cc_start: 0.8402 (mtp85) cc_final: 0.7634 (ttt90) REVERT: H 51 ASP cc_start: 0.8612 (p0) cc_final: 0.8371 (p0) REVERT: H 83 TYR cc_start: 0.8517 (m-10) cc_final: 0.8255 (m-10) REVERT: H 105 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7720 (tm-30) REVERT: H 106 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9113 (mt) REVERT: H 113 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8901 (mt-10) REVERT: K 1 MET cc_start: 0.7570 (tmm) cc_final: 0.7226 (tmm) REVERT: K 38 MET cc_start: 0.9112 (mtt) cc_final: 0.8816 (tpt) REVERT: K 41 ASN cc_start: 0.8592 (m-40) cc_final: 0.8335 (p0) REVERT: K 87 ASP cc_start: 0.8844 (p0) cc_final: 0.8600 (t0) REVERT: K 120 VAL cc_start: 0.7596 (OUTLIER) cc_final: 0.7296 (p) REVERT: K 136 ARG cc_start: 0.9339 (ppt170) cc_final: 0.9082 (tmm-80) REVERT: K 145 TYR cc_start: 0.7581 (m-80) cc_final: 0.7339 (m-80) REVERT: L 20 MET cc_start: 0.7092 (mmt) cc_final: 0.6672 (mmt) REVERT: L 50 CYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7606 (t) REVERT: L 73 ASN cc_start: 0.7479 (t0) cc_final: 0.7255 (m110) outliers start: 20 outliers final: 13 residues processed: 219 average time/residue: 0.1249 time to fit residues: 39.2916 Evaluate side-chains 217 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 45 TYR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 143 GLN Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 50 CYS Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 36 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 109 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 68 ASN G 38 ASN D 47 GLN K 143 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.050051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.033856 restraints weight = 81334.956| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.98 r_work: 0.2584 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15173 Z= 0.150 Angle : 0.646 12.427 21790 Z= 0.371 Chirality : 0.041 0.250 2489 Planarity : 0.004 0.060 1746 Dihedral : 29.864 173.378 4381 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.42 % Allowed : 18.22 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.27), residues: 1033 helix: 2.40 (0.20), residues: 647 sheet: -0.59 (0.93), residues: 24 loop : -0.54 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 136 TYR 0.066 0.002 TYR D 83 PHE 0.012 0.001 PHE E 67 TRP 0.017 0.002 TRP K 141 HIS 0.004 0.001 HIS K 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (15165) covalent geometry : angle 0.64377 / 0.37 (21781) hydrogen bonds : bond 0.08561 / 5.80 ( 827) hydrogen bonds : angle 3.27762 / 2.40 ( 2029) metal coordination : bond 0.00491 / 0.22 ( 8) metal coordination : angle 2.49740 / 1.35 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9097 (pm20) cc_final: 0.8763 (pm20) REVERT: A 73 GLU cc_start: 0.9443 (tm-30) cc_final: 0.9167 (tm-30) REVERT: A 79 LYS cc_start: 0.9141 (tptm) cc_final: 0.8637 (tptp) REVERT: C 24 GLN cc_start: 0.9294 (mm-40) cc_final: 0.8813 (mp10) REVERT: C 56 GLU cc_start: 0.9296 (tt0) cc_final: 0.8896 (tt0) REVERT: E 73 GLU cc_start: 0.8717 (tt0) cc_final: 0.8466 (tt0) REVERT: F 91 LYS cc_start: 0.9442 (ttmt) cc_final: 0.9124 (ttpt) REVERT: G 61 GLU cc_start: 0.8996 (tp30) cc_final: 0.8785 (tp30) REVERT: G 64 GLU cc_start: 0.9342 (OUTLIER) cc_final: 0.9055 (pp20) REVERT: D 83 TYR cc_start: 0.8167 (m-80) cc_final: 0.7932 (m-80) REVERT: D 93 GLU cc_start: 0.8794 (mp0) cc_final: 0.8547 (mp0) REVERT: H 33 ARG cc_start: 0.8398 (mtp85) cc_final: 0.7581 (ttt180) REVERT: H 51 ASP cc_start: 0.8622 (p0) cc_final: 0.8384 (p0) REVERT: H 83 TYR cc_start: 0.8535 (m-10) cc_final: 0.8261 (m-10) REVERT: H 105 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7718 (tm-30) REVERT: H 106 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9108 (mt) REVERT: H 113 GLU cc_start: 0.9290 (mm-30) cc_final: 0.8913 (mt-10) REVERT: K 1 MET cc_start: 0.7545 (tmm) cc_final: 0.7198 (tmm) REVERT: K 38 MET cc_start: 0.9109 (mtt) cc_final: 0.8795 (tpt) REVERT: K 41 ASN cc_start: 0.8552 (m-40) cc_final: 0.8312 (p0) REVERT: K 87 ASP cc_start: 0.8854 (p0) cc_final: 0.8632 (t0) REVERT: K 120 VAL cc_start: 0.7574 (OUTLIER) cc_final: 0.7261 (p) REVERT: K 136 ARG cc_start: 0.9335 (ppt170) cc_final: 0.9077 (tmm-80) REVERT: K 145 TYR cc_start: 0.7495 (m-80) cc_final: 0.7222 (m-80) REVERT: L 20 MET cc_start: 0.7104 (mmt) cc_final: 0.6673 (mmt) REVERT: L 50 CYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7624 (t) REVERT: L 73 ASN cc_start: 0.7479 (t0) cc_final: 0.7267 (m110) outliers start: 21 outliers final: 16 residues processed: 210 average time/residue: 0.1140 time to fit residues: 34.7029 Evaluate side-chains 214 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 45 TYR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 143 GLN Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 50 CYS Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 36 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 102 optimal weight: 30.0000 chunk 105 optimal weight: 0.4980 chunk 127 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 68 ASN K 143 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.049901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.033697 restraints weight = 81186.898| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.97 r_work: 0.2580 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15173 Z= 0.165 Angle : 0.660 12.413 21790 Z= 0.377 Chirality : 0.042 0.249 2489 Planarity : 0.005 0.085 1746 Dihedral : 29.893 173.567 4381 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.54 % Allowed : 18.11 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % 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: 1033 helix: 2.33 (0.20), residues: 650 sheet: -0.69 (0.92), residues: 24 loop : -0.50 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 136 TYR 0.079 0.002 TYR D 83 PHE 0.012 0.001 PHE E 67 TRP 0.010 0.002 TRP K 141 HIS 0.004 0.001 HIS K 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 (15165) covalent geometry : angle 0.65848 / 0.38 (21781) hydrogen bonds : bond 0.08510 / 5.76 ( 827) hydrogen bonds : angle 3.29611 / 2.41 ( 2029) metal coordination : bond 0.00493 / 0.22 ( 8) metal coordination : angle 2.41990 / 1.32 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9091 (pm20) cc_final: 0.8761 (pm20) REVERT: A 73 GLU cc_start: 0.9437 (tm-30) cc_final: 0.9145 (tm-30) REVERT: A 79 LYS cc_start: 0.9169 (tptm) cc_final: 0.8686 (tptp) REVERT: C 24 GLN cc_start: 0.9311 (mm-40) cc_final: 0.8804 (mp10) REVERT: C 56 GLU cc_start: 0.9290 (tt0) cc_final: 0.8885 (tt0) REVERT: C 95 LYS cc_start: 0.9645 (tptt) cc_final: 0.9423 (tptp) REVERT: E 73 GLU cc_start: 0.8695 (tt0) cc_final: 0.8447 (tt0) REVERT: F 91 LYS cc_start: 0.9444 (ttmt) cc_final: 0.9135 (ttpt) REVERT: G 61 GLU cc_start: 0.9003 (tp30) cc_final: 0.8787 (tp30) REVERT: G 64 GLU cc_start: 0.9352 (OUTLIER) cc_final: 0.9069 (pp20) REVERT: D 93 GLU cc_start: 0.8817 (mp0) cc_final: 0.8577 (mp0) REVERT: H 33 ARG cc_start: 0.8398 (mtp85) cc_final: 0.7628 (ttt90) REVERT: H 51 ASP cc_start: 0.8630 (p0) cc_final: 0.8404 (p0) REVERT: H 83 TYR cc_start: 0.8532 (m-10) cc_final: 0.8257 (m-10) REVERT: H 113 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8921 (mt-10) REVERT: K 1 MET cc_start: 0.7472 (tmm) cc_final: 0.7141 (tmm) REVERT: K 38 MET cc_start: 0.9102 (mtt) cc_final: 0.8788 (tpt) REVERT: K 87 ASP cc_start: 0.8781 (p0) cc_final: 0.8551 (t0) REVERT: K 120 VAL cc_start: 0.7452 (OUTLIER) cc_final: 0.7137 (p) REVERT: K 136 ARG cc_start: 0.9344 (ppt170) cc_final: 0.9120 (tmm-80) REVERT: K 145 TYR cc_start: 0.7560 (m-80) cc_final: 0.7278 (m-80) REVERT: L 20 MET cc_start: 0.7114 (mmt) cc_final: 0.6679 (mmt) REVERT: L 50 CYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7579 (t) REVERT: L 73 ASN cc_start: 0.7480 (t0) cc_final: 0.7267 (m110) outliers start: 22 outliers final: 18 residues processed: 208 average time/residue: 0.1072 time to fit residues: 32.6433 Evaluate side-chains 214 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 45 TYR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 143 GLN Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 50 CYS Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 36 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 126 optimal weight: 40.0000 chunk 127 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN C 68 ASN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.049654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.033452 restraints weight = 81555.986| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.95 r_work: 0.2570 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15173 Z= 0.181 Angle : 0.665 12.884 21790 Z= 0.378 Chirality : 0.042 0.247 2489 Planarity : 0.005 0.059 1746 Dihedral : 29.959 173.858 4381 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.08 % Allowed : 19.15 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % 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: 1033 helix: 2.27 (0.21), residues: 650 sheet: -0.79 (0.91), residues: 24 loop : -0.46 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 131 TYR 0.085 0.003 TYR D 83 PHE 0.012 0.001 PHE E 67 TRP 0.012 0.002 TRP K 141 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.18 (15165) covalent geometry : angle 0.66321 / 0.38 (21781) hydrogen bonds : bond 0.08439 / 5.72 ( 827) hydrogen bonds : angle 3.34336 / 2.45 ( 2029) metal coordination : bond 0.00501 / 0.22 ( 8) metal coordination : angle 2.47093 / 1.36 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3226.42 seconds wall clock time: 55 minutes 50.91 seconds (3350.91 seconds total)