Starting phenix.real_space_refine on Fri Aug 7 01:01:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8u14_41801/08_2026/8u14_41801.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u14_41801/08_2026/8u14_41801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8u14_41801/08_2026/8u14_41801.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8u14_41801/08_2026/8u14_41801.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u14_41801/08_2026/8u14_41801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u14_41801/08_2026/8u14_41801.map" model { file = "/net/cci-nas-00/data/ceres_data/8u14_41801/08_2026/8u14_41801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u14_41801/08_2026/8u14_41801.cif" } resolution = 3.9 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 5925 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 293 5.49 5 S 32 5.16 5 C 7885 2.51 5 N 2608 2.21 5 O 3175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13995 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 751 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 706 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Conformer: "B" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} bond proxies already assigned to first conformer: 713 Chain: "L" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1176 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "C" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 843 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10611 SG CYS K 31 77.501 68.587 45.284 1.00155.98 S ATOM 10761 SG CYS K 51 77.762 71.763 47.414 1.00157.25 S ATOM 10785 SG CYS K 54 76.542 71.999 43.785 1.00157.66 S ATOM 10502 SG CYS K 16 86.876 72.181 56.653 1.00201.51 S ATOM 10520 SG CYS K 19 87.004 73.675 59.834 1.00219.51 S ATOM 10650 SG CYS K 36 84.987 70.188 59.204 1.00192.64 S ATOM 10672 SG CYS K 39 83.453 73.315 58.539 1.00199.41 S Time building chain proxies: 3.12, per 1000 atoms: 0.22 Number of scatterers: 13995 At special positions: 0 Unit cell: (107.898, 126.395, 118.174, 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 32 16.00 P 293 15.00 O 3175 8.00 N 2608 7.00 C 7885 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 442.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " Number of angles added : 9 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 8 sheets defined 65.5% alpha, 3.3% beta 140 base pairs and 241 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.702A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.768A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.639A 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: 3.799A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 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 removed outlier: 3.653A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.528A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.365A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.514A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (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 Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'K' and resid 36 through 45 removed outlier: 3.664A pdb=" N GLU K 45 " --> pdb=" O GLN K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 67 removed outlier: 4.642A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 92 removed outlier: 3.935A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 Processing helix chain 'L' and resid 86 through 91 removed outlier: 3.983A pdb=" N ARG L 90 " --> pdb=" O LEU L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.535A pdb=" N ALA L 124 " --> pdb=" O VAL L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 147 removed outlier: 3.700A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA L 146 " --> pdb=" O THR L 142 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET L 147 " --> pdb=" O GLN L 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.395A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.898A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 74 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 98 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.634A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.214A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.600A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.393A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AA7, first strand: chain 'K' and resid 27 through 28 removed outlier: 3.555A pdb=" N VAL K 27 " --> pdb=" O LEU K 35 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 21 through 25 486 hydrogen bonds defined for protein. 1442 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 358 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 241 stacking parallelities Total time for adding SS restraints: 2.85 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3398 1.34 - 1.46: 4244 1.46 - 1.58: 6583 1.58 - 1.70: 584 1.70 - 1.82: 46 Bond restraints: 14855 Sorted by residual: bond pdb=" C3' DT J 13 " pdb=" C2' DT J 13 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DT J -57 " pdb=" C2' DT J -57 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DG I 40 " pdb=" C2' DG I 40 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DC I -18 " pdb=" C2' DC I -18 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 14850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 20068 1.65 - 3.29: 1175 3.29 - 4.94: 69 4.94 - 6.59: 16 6.59 - 8.23: 6 Bond angle restraints: 21334 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 113.53 108.56 4.97 9.80e-01 1.04e+00 2.57e+01 angle pdb=" O4' DT I -26 " pdb=" C4' DT I -26 " pdb=" C3' DT I -26 " ideal model delta sigma weight residual 106.00 103.31 2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT J -17 " pdb=" C4 DT J -17 " pdb=" O4 DT J -17 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" O4' DG J -49 " pdb=" C4' DG J -49 " pdb=" C3' DG J -49 " ideal model delta sigma weight residual 106.00 103.42 2.58 6.00e-01 2.78e+00 1.84e+01 ... (remaining 21329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.61: 6645 31.61 - 63.22: 1529 63.22 - 94.84: 42 94.84 - 126.45: 0 126.45 - 158.06: 2 Dihedral angle restraints: 8218 sinusoidal: 5288 harmonic: 2930 Sorted by residual: dihedral pdb=" CA ASN B 25 " pdb=" C ASN B 25 " pdb=" N ILE B 26 " pdb=" CA ILE B 26 " ideal model delta harmonic sigma weight residual 180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 61.94 158.06 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 65.92 154.08 1 3.50e+01 8.16e-04 1.49e+01 ... (remaining 8215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1452 0.034 - 0.069: 662 0.069 - 0.103: 238 0.103 - 0.138: 61 0.138 - 0.172: 5 Chirality restraints: 2418 Sorted by residual: chirality pdb=" CA GLU F 63 " pdb=" N GLU F 63 " pdb=" C GLU F 63 " pdb=" CB GLU F 63 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" P DT J -16 " pdb=" OP1 DT J -16 " pdb=" OP2 DT J -16 " pdb=" O5' DT J -16 " both_signs ideal model delta sigma weight residual True 2.34 -2.48 -0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 2415 not shown) Planarity restraints: 1692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.024 2.00e-02 2.50e+03 1.04e-02 2.98e+00 pdb=" N9 DA I -35 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C LYS F 59 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS F 59 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL F 60 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 73 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" CD GLU A 73 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU A 73 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A 73 " -0.010 2.00e-02 2.50e+03 ... (remaining 1689 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 466 2.68 - 3.23: 13143 3.23 - 3.79: 27192 3.79 - 4.34: 32816 4.34 - 4.90: 46740 Nonbonded interactions: 120357 Sorted by model distance: nonbonded pdb=" O ARG K 63 " pdb=" NH1 ARG K 67 " model vdw 2.124 3.120 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.150 2.496 nonbonded pdb=" OE1 GLN D 95 " pdb=" OH TYR C 50 " model vdw 2.160 3.040 nonbonded pdb=" NE2 HIS B 75 " pdb=" OE1 GLU D 93 " model vdw 2.204 3.120 nonbonded pdb=" OE2 GLU H 105 " pdb=" NH1 ARG K 67 " model vdw 2.223 3.120 ... (remaining 120352 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 119) } ncs_group { reference = (chain 'D' and resid 31 through 123) 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.210 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.005 0.040 14865 Z= 0.482 Angle : 0.801 12.911 21349 Z= 0.646 Chirality : 0.044 0.172 2418 Planarity : 0.004 0.041 1690 Dihedral : 26.360 158.059 6320 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.27), residues: 987 helix: 1.25 (0.21), residues: 623 sheet: 0.72 (0.98), residues: 24 loop : -1.10 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 36 TYR 0.024 0.001 TYR F 88 PHE 0.017 0.001 PHE E 78 TRP 0.011 0.001 TRP K 61 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.48 (14855) covalent geometry : angle 0.78413 / 0.65 (21334) hydrogen bonds : bond 0.10380 / 6.51 ( 844) hydrogen bonds : angle 4.37418 / 3.14 ( 2154) metal coordination : bond 0.00526 / 0.30 ( 8) metal coordination : angle 7.88243 / 3.35 ( 9) link_TRANS : bond 0.00188 / 0.09 ( 2) link_TRANS : angle 0.84845 / 0.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8750 (m-30) cc_final: 0.8495 (m-30) REVERT: A 125 GLN cc_start: 0.8605 (mp10) cc_final: 0.7989 (mp10) REVERT: D 59 MET cc_start: 0.8760 (tpt) cc_final: 0.8525 (tpt) REVERT: E 73 GLU cc_start: 0.8223 (mt-10) cc_final: 0.8009 (mt-10) REVERT: E 77 ASP cc_start: 0.8106 (m-30) cc_final: 0.7873 (m-30) REVERT: E 120 MET cc_start: 0.8851 (mmm) cc_final: 0.8432 (mmm) REVERT: F 31 LYS cc_start: 0.9471 (tttm) cc_final: 0.9057 (tptm) REVERT: F 64 ASN cc_start: 0.8753 (m-40) cc_final: 0.8429 (m110) REVERT: H 47 GLN cc_start: 0.8800 (tt0) cc_final: 0.8495 (tm-30) REVERT: H 48 VAL cc_start: 0.9346 (p) cc_final: 0.9145 (p) REVERT: H 71 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8207 (tm-30) REVERT: H 85 LYS cc_start: 0.9364 (mtmm) cc_final: 0.9033 (mtmm) REVERT: K 18 ILE cc_start: 0.8706 (mm) cc_final: 0.8483 (mm) REVERT: K 41 GLN cc_start: 0.9313 (mt0) cc_final: 0.8888 (mp10) REVERT: C 56 GLU cc_start: 0.9069 (tp30) cc_final: 0.8813 (tp30) REVERT: C 90 ASP cc_start: 0.8551 (t70) cc_final: 0.8319 (t0) REVERT: G 92 GLU cc_start: 0.7885 (pt0) cc_final: 0.7274 (pt0) REVERT: G 104 GLN cc_start: 0.8553 (tt0) cc_final: 0.7766 (tm-30) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.1445 time to fit residues: 70.5092 Evaluate side-chains 280 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 40.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 76 GLN E 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.081653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.058473 restraints weight = 67348.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.060092 restraints weight = 33563.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.061241 restraints weight = 22690.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061930 restraints weight = 18071.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.062225 restraints weight = 15807.829| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14865 Z= 0.199 Angle : 0.747 15.286 21349 Z= 0.418 Chirality : 0.046 0.242 2418 Planarity : 0.005 0.058 1690 Dihedral : 29.809 159.429 4321 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.45 % Allowed : 17.37 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.26), residues: 987 helix: 1.27 (0.21), residues: 630 sheet: 0.40 (0.99), residues: 24 loop : -1.31 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 136 TYR 0.029 0.002 TYR F 88 PHE 0.018 0.002 PHE A 104 TRP 0.017 0.002 TRP K 61 HIS 0.005 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.20 (14855) covalent geometry : angle 0.72453 / 0.42 (21334) hydrogen bonds : bond 0.05516 / 3.61 ( 844) hydrogen bonds : angle 4.00271 / 2.92 ( 2154) metal coordination : bond 0.00789 / 0.37 ( 8) metal coordination : angle 8.80533 / 3.74 ( 9) link_TRANS : bond 0.00095 / 0.05 ( 2) link_TRANS : angle 0.57897 / 0.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 302 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8992 (m-30) cc_final: 0.8703 (m-30) REVERT: A 125 GLN cc_start: 0.8561 (mp10) cc_final: 0.8193 (mp10) REVERT: B 84 MET cc_start: 0.9311 (tpp) cc_final: 0.8962 (tpp) REVERT: D 33 ARG cc_start: 0.8816 (ttm110) cc_final: 0.8419 (tpp80) REVERT: E 50 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8640 (mm-30) REVERT: E 120 MET cc_start: 0.8751 (mmm) cc_final: 0.8345 (mmm) REVERT: F 27 GLN cc_start: 0.9201 (mp10) cc_final: 0.8966 (mp10) REVERT: F 31 LYS cc_start: 0.9505 (tttm) cc_final: 0.9169 (tttp) REVERT: F 35 ARG cc_start: 0.9351 (ttm110) cc_final: 0.9088 (ttm110) REVERT: F 84 MET cc_start: 0.8214 (tpp) cc_final: 0.7934 (tpp) REVERT: H 47 GLN cc_start: 0.8859 (tt0) cc_final: 0.8511 (tm-30) REVERT: H 71 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8453 (tm-30) REVERT: K 63 ARG cc_start: 0.8588 (ptm-80) cc_final: 0.8193 (ptm-80) REVERT: K 68 ARG cc_start: 0.6763 (mpp-170) cc_final: 0.6245 (mpp80) REVERT: K 86 ARG cc_start: 0.9360 (pmt170) cc_final: 0.9065 (pmt170) REVERT: C 56 GLU cc_start: 0.9141 (tp30) cc_final: 0.8856 (tp30) REVERT: C 73 ASN cc_start: 0.9506 (t0) cc_final: 0.9235 (t0) REVERT: C 90 ASP cc_start: 0.8567 (t70) cc_final: 0.8225 (t0) REVERT: G 90 ASP cc_start: 0.8576 (t70) cc_final: 0.8144 (t70) REVERT: G 104 GLN cc_start: 0.8686 (tt0) cc_final: 0.7874 (tm-30) outliers start: 21 outliers final: 12 residues processed: 311 average time/residue: 0.1371 time to fit residues: 59.1806 Evaluate side-chains 296 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 284 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 46 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 117 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.082001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.059157 restraints weight = 76947.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.060933 restraints weight = 34971.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.062173 restraints weight = 22237.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.062920 restraints weight = 16981.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.063209 restraints weight = 14499.038| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14865 Z= 0.161 Angle : 0.703 12.255 21349 Z= 0.397 Chirality : 0.044 0.251 2418 Planarity : 0.004 0.037 1690 Dihedral : 29.915 158.711 4321 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.68 % Allowed : 20.75 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.26), residues: 987 helix: 1.31 (0.20), residues: 629 sheet: 0.27 (1.02), residues: 24 loop : -1.30 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 67 TYR 0.028 0.002 TYR B 88 PHE 0.014 0.002 PHE A 104 TRP 0.012 0.001 TRP K 61 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 (14855) covalent geometry : angle 0.68610 / 0.40 (21334) hydrogen bonds : bond 0.04858 / 3.15 ( 844) hydrogen bonds : angle 3.82336 / 2.79 ( 2154) metal coordination : bond 0.00816 / 0.39 ( 8) metal coordination : angle 7.45759 / 3.17 ( 9) link_TRANS : bond 0.00043 / 0.02 ( 2) link_TRANS : angle 0.17256 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 297 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8495 (pp20) cc_final: 0.7996 (pp20) REVERT: A 53 ARG cc_start: 0.8661 (tmm-80) cc_final: 0.7933 (tmm-80) REVERT: A 108 ASN cc_start: 0.9172 (t0) cc_final: 0.8966 (t0) REVERT: A 125 GLN cc_start: 0.8436 (mp10) cc_final: 0.8113 (mp10) REVERT: B 84 MET cc_start: 0.9214 (tpp) cc_final: 0.8673 (tpp) REVERT: B 88 TYR cc_start: 0.9018 (m-10) cc_final: 0.8791 (m-80) REVERT: D 33 ARG cc_start: 0.8798 (ttm110) cc_final: 0.8419 (tpp80) REVERT: E 73 GLU cc_start: 0.8779 (tt0) cc_final: 0.8500 (tt0) REVERT: E 77 ASP cc_start: 0.8254 (m-30) cc_final: 0.7999 (m-30) REVERT: E 120 MET cc_start: 0.8778 (mmm) cc_final: 0.8296 (mmm) REVERT: E 126 LEU cc_start: 0.9583 (tt) cc_final: 0.9366 (tp) REVERT: F 31 LYS cc_start: 0.9459 (tttm) cc_final: 0.8902 (tttp) REVERT: F 35 ARG cc_start: 0.9293 (ttm110) cc_final: 0.8842 (ttm110) REVERT: F 39 ARG cc_start: 0.9326 (tpp80) cc_final: 0.8972 (mmt-90) REVERT: F 64 ASN cc_start: 0.8603 (m-40) cc_final: 0.8264 (m110) REVERT: F 84 MET cc_start: 0.8126 (tpp) cc_final: 0.7807 (tpp) REVERT: F 92 ARG cc_start: 0.8655 (ttp80) cc_final: 0.8175 (ttp80) REVERT: H 47 GLN cc_start: 0.8811 (tt0) cc_final: 0.8502 (tm-30) REVERT: H 71 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8482 (tm-30) REVERT: H 85 LYS cc_start: 0.9332 (mtmm) cc_final: 0.9116 (mtmm) REVERT: H 93 GLU cc_start: 0.8879 (mp0) cc_final: 0.8620 (mp0) REVERT: K 68 ARG cc_start: 0.6821 (mpp-170) cc_final: 0.6285 (mpp80) REVERT: K 86 ARG cc_start: 0.9372 (pmt170) cc_final: 0.9149 (pmt170) REVERT: L 32 HIS cc_start: 0.8837 (OUTLIER) cc_final: 0.8302 (m-70) REVERT: L 63 LYS cc_start: 0.7576 (tptt) cc_final: 0.7221 (tppt) REVERT: C 56 GLU cc_start: 0.9083 (tp30) cc_final: 0.8702 (tp30) REVERT: C 73 ASN cc_start: 0.9481 (t0) cc_final: 0.9217 (t0) REVERT: C 90 ASP cc_start: 0.8538 (t70) cc_final: 0.8172 (t0) REVERT: G 57 TYR cc_start: 0.8724 (t80) cc_final: 0.8508 (t80) REVERT: G 90 ASP cc_start: 0.8530 (t70) cc_final: 0.7949 (t70) REVERT: G 104 GLN cc_start: 0.8736 (tt0) cc_final: 0.7830 (tm-30) outliers start: 23 outliers final: 16 residues processed: 307 average time/residue: 0.1317 time to fit residues: 56.7756 Evaluate side-chains 297 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 280 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 55 optimal weight: 20.0000 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 chunk 83 optimal weight: 0.2980 chunk 68 optimal weight: 20.0000 chunk 23 optimal weight: 0.1980 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.081897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.058585 restraints weight = 78023.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.060394 restraints weight = 35945.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.061573 restraints weight = 23056.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.062334 restraints weight = 17926.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.062656 restraints weight = 15448.509| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14865 Z= 0.160 Angle : 0.695 11.943 21349 Z= 0.391 Chirality : 0.044 0.259 2418 Planarity : 0.004 0.038 1690 Dihedral : 29.980 159.441 4321 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.15 % Allowed : 22.73 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.26), residues: 987 helix: 1.39 (0.21), residues: 629 sheet: 0.15 (1.04), residues: 24 loop : -1.29 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 139 TYR 0.025 0.002 TYR F 88 PHE 0.013 0.001 PHE K 40 TRP 0.012 0.001 TRP K 61 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (14855) covalent geometry : angle 0.68045 / 0.39 (21334) hydrogen bonds : bond 0.04738 / 3.10 ( 844) hydrogen bonds : angle 3.73990 / 2.72 ( 2154) metal coordination : bond 0.00926 / 0.45 ( 8) metal coordination : angle 6.98920 / 2.96 ( 9) link_TRANS : bond 0.00054 / 0.03 ( 2) link_TRANS : angle 0.23665 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 299 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8788 (tp) cc_final: 0.8491 (tp) REVERT: D 33 ARG cc_start: 0.8818 (ttm110) cc_final: 0.8445 (tpp80) REVERT: E 73 GLU cc_start: 0.8790 (tt0) cc_final: 0.8524 (tt0) REVERT: E 77 ASP cc_start: 0.8241 (m-30) cc_final: 0.7997 (m-30) REVERT: E 120 MET cc_start: 0.8882 (mmm) cc_final: 0.8272 (mmm) REVERT: F 31 LYS cc_start: 0.9438 (tttm) cc_final: 0.8840 (tttp) REVERT: F 35 ARG cc_start: 0.9259 (ttm110) cc_final: 0.8783 (ttm110) REVERT: F 39 ARG cc_start: 0.9322 (tpp80) cc_final: 0.8993 (mmt-90) REVERT: F 84 MET cc_start: 0.8125 (tpp) cc_final: 0.7912 (tpp) REVERT: F 92 ARG cc_start: 0.8698 (ttp80) cc_final: 0.8203 (ttp80) REVERT: H 47 GLN cc_start: 0.8828 (tt0) cc_final: 0.8497 (tm-30) REVERT: H 85 LYS cc_start: 0.9347 (mtmm) cc_final: 0.9137 (mtmm) REVERT: K 68 ARG cc_start: 0.6933 (mpp-170) cc_final: 0.6385 (mpp80) REVERT: L 32 HIS cc_start: 0.8800 (OUTLIER) cc_final: 0.8258 (m-70) REVERT: L 63 LYS cc_start: 0.7573 (tptt) cc_final: 0.7269 (tppt) REVERT: C 73 ASN cc_start: 0.9445 (t0) cc_final: 0.9171 (t0) REVERT: C 90 ASP cc_start: 0.8482 (t70) cc_final: 0.8147 (t0) REVERT: G 84 GLN cc_start: 0.9117 (tp-100) cc_final: 0.8486 (tp-100) REVERT: G 104 GLN cc_start: 0.8737 (tt0) cc_final: 0.7780 (tm-30) outliers start: 27 outliers final: 20 residues processed: 310 average time/residue: 0.1313 time to fit residues: 57.0551 Evaluate side-chains 304 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 283 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 60 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 91 optimal weight: 30.0000 chunk 118 optimal weight: 6.9990 chunk 12 optimal weight: 0.1980 chunk 6 optimal weight: 0.6980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.080775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.057511 restraints weight = 63660.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.059005 restraints weight = 32701.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060046 restraints weight = 22377.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.060701 restraints weight = 18007.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.060976 restraints weight = 15909.343| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14865 Z= 0.186 Angle : 0.720 10.909 21349 Z= 0.403 Chirality : 0.044 0.270 2418 Planarity : 0.005 0.040 1690 Dihedral : 30.081 159.679 4321 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.31 % Allowed : 23.78 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.27), residues: 987 helix: 1.34 (0.21), residues: 629 sheet: 0.09 (1.06), residues: 24 loop : -1.28 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 63 TYR 0.041 0.002 TYR B 88 PHE 0.014 0.001 PHE A 104 TRP 0.018 0.001 TRP K 61 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.19 (14855) covalent geometry : angle 0.70686 / 0.40 (21334) hydrogen bonds : bond 0.04954 / 3.28 ( 844) hydrogen bonds : angle 3.79550 / 2.77 ( 2154) metal coordination : bond 0.01357 / 0.66 ( 8) metal coordination : angle 6.83586 / 2.98 ( 9) link_TRANS : bond 0.00128 / 0.06 ( 2) link_TRANS : angle 0.27004 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 298 time to evaluate : 0.308 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 50 GLU cc_start: 0.8515 (pp20) cc_final: 0.7515 (pp20) REVERT: A 53 ARG cc_start: 0.8660 (tmm-80) cc_final: 0.7667 (tmm-80) REVERT: A 54 TYR cc_start: 0.7393 (m-80) cc_final: 0.6300 (m-10) REVERT: A 125 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8800 (mm-40) REVERT: D 33 ARG cc_start: 0.8846 (ttm110) cc_final: 0.8486 (tpp80) REVERT: E 73 GLU cc_start: 0.8733 (tt0) cc_final: 0.8471 (tt0) REVERT: E 77 ASP cc_start: 0.8226 (m-30) cc_final: 0.8000 (m-30) REVERT: E 120 MET cc_start: 0.8839 (mmm) cc_final: 0.8220 (mmm) REVERT: F 31 LYS cc_start: 0.9404 (tttm) cc_final: 0.8728 (tttp) REVERT: F 35 ARG cc_start: 0.9256 (ttm110) cc_final: 0.8830 (ttm110) REVERT: F 84 MET cc_start: 0.8192 (tpp) cc_final: 0.7966 (tpp) REVERT: F 92 ARG cc_start: 0.8745 (ttp80) cc_final: 0.8240 (ttp80) REVERT: H 47 GLN cc_start: 0.8832 (tt0) cc_final: 0.8515 (tm-30) REVERT: L 32 HIS cc_start: 0.8808 (OUTLIER) cc_final: 0.8286 (m-70) REVERT: L 63 LYS cc_start: 0.7551 (tptt) cc_final: 0.7238 (tppt) REVERT: C 56 GLU cc_start: 0.9074 (tp30) cc_final: 0.8681 (tp30) REVERT: C 73 ASN cc_start: 0.9425 (t0) cc_final: 0.9136 (t0) REVERT: C 90 ASP cc_start: 0.8531 (t70) cc_final: 0.8200 (t0) REVERT: G 84 GLN cc_start: 0.9139 (tp-100) cc_final: 0.8445 (tp-100) outliers start: 37 outliers final: 23 residues processed: 313 average time/residue: 0.1355 time to fit residues: 58.7704 Evaluate side-chains 308 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 284 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 78 optimal weight: 30.0000 chunk 56 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.080331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.057365 restraints weight = 73906.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.059077 restraints weight = 34423.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.060151 restraints weight = 22236.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.060915 restraints weight = 17392.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.061256 restraints weight = 14933.411| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14865 Z= 0.185 Angle : 0.732 10.909 21349 Z= 0.406 Chirality : 0.045 0.275 2418 Planarity : 0.005 0.056 1690 Dihedral : 30.148 159.415 4321 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.73 % Allowed : 25.52 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.27), residues: 987 helix: 1.31 (0.21), residues: 629 sheet: 0.04 (1.08), residues: 24 loop : -1.30 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 67 TYR 0.059 0.002 TYR B 88 PHE 0.013 0.001 PHE L 56 TRP 0.015 0.001 TRP K 61 HIS 0.004 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (14855) covalent geometry : angle 0.71978 / 0.41 (21334) hydrogen bonds : bond 0.04918 / 3.25 ( 844) hydrogen bonds : angle 3.81194 / 2.78 ( 2154) metal coordination : bond 0.01474 / 0.72 ( 8) metal coordination : angle 6.56594 / 2.83 ( 9) link_TRANS : bond 0.00122 / 0.06 ( 2) link_TRANS : angle 0.27113 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 299 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8484 (pp20) cc_final: 0.7470 (pp20) REVERT: A 53 ARG cc_start: 0.8616 (tmm-80) cc_final: 0.8049 (tmm-80) REVERT: D 33 ARG cc_start: 0.8822 (ttm110) cc_final: 0.8467 (tpp80) REVERT: E 73 GLU cc_start: 0.8733 (tt0) cc_final: 0.8427 (tt0) REVERT: E 77 ASP cc_start: 0.8127 (m-30) cc_final: 0.7905 (m-30) REVERT: E 120 MET cc_start: 0.8890 (mmm) cc_final: 0.8358 (mmm) REVERT: F 31 LYS cc_start: 0.9396 (tttm) cc_final: 0.8721 (tttp) REVERT: F 35 ARG cc_start: 0.9243 (ttm110) cc_final: 0.8798 (ttm110) REVERT: F 39 ARG cc_start: 0.9358 (tpp80) cc_final: 0.9126 (mmt-90) REVERT: F 67 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7863 (tpm170) REVERT: F 84 MET cc_start: 0.8236 (tpp) cc_final: 0.7995 (tpp) REVERT: F 92 ARG cc_start: 0.8757 (ttp80) cc_final: 0.8129 (ttp80) REVERT: H 47 GLN cc_start: 0.8845 (tt0) cc_final: 0.8520 (tm-30) REVERT: H 71 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8470 (tm-30) REVERT: L 63 LYS cc_start: 0.7571 (tptt) cc_final: 0.7233 (tppt) REVERT: C 56 GLU cc_start: 0.9053 (tp30) cc_final: 0.8671 (tp30) REVERT: C 73 ASN cc_start: 0.9394 (t0) cc_final: 0.9104 (t0) REVERT: C 90 ASP cc_start: 0.8549 (t70) cc_final: 0.8184 (t0) REVERT: G 91 GLU cc_start: 0.8271 (pm20) cc_final: 0.7971 (pm20) outliers start: 32 outliers final: 25 residues processed: 312 average time/residue: 0.1379 time to fit residues: 59.8032 Evaluate side-chains 310 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 284 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 96 optimal weight: 6.9990 chunk 74 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 90 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.080605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.055847 restraints weight = 106492.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.057825 restraints weight = 43667.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.059145 restraints weight = 26393.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.059962 restraints weight = 19720.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.060325 restraints weight = 16695.079| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14865 Z= 0.182 Angle : 0.731 11.357 21349 Z= 0.404 Chirality : 0.045 0.278 2418 Planarity : 0.004 0.044 1690 Dihedral : 30.187 159.530 4321 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.43 % Allowed : 24.94 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.27), residues: 987 helix: 1.28 (0.20), residues: 629 sheet: 0.10 (1.10), residues: 24 loop : -1.27 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 67 TYR 0.062 0.002 TYR B 88 PHE 0.015 0.002 PHE L 56 TRP 0.018 0.001 TRP K 61 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (14855) covalent geometry : angle 0.71860 / 0.40 (21334) hydrogen bonds : bond 0.04853 / 3.21 ( 844) hydrogen bonds : angle 3.82748 / 2.78 ( 2154) metal coordination : bond 0.01468 / 0.72 ( 8) metal coordination : angle 6.54053 / 2.83 ( 9) link_TRANS : bond 0.00112 / 0.05 ( 2) link_TRANS : angle 0.25596 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 290 time to evaluate : 0.378 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: D 33 ARG cc_start: 0.8797 (ttm110) cc_final: 0.8483 (tpp80) REVERT: E 73 GLU cc_start: 0.8758 (tt0) cc_final: 0.8442 (tt0) REVERT: E 77 ASP cc_start: 0.8180 (m-30) cc_final: 0.7954 (m-30) REVERT: E 120 MET cc_start: 0.8841 (mmm) cc_final: 0.8300 (mmm) REVERT: F 39 ARG cc_start: 0.9362 (tpp80) cc_final: 0.9130 (mmt-90) REVERT: H 47 GLN cc_start: 0.8818 (tt0) cc_final: 0.8516 (tm-30) REVERT: H 71 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8472 (tm-30) REVERT: H 105 GLU cc_start: 0.7003 (pm20) cc_final: 0.6692 (pm20) REVERT: H 116 LYS cc_start: 0.9084 (mmmt) cc_final: 0.8619 (mmtp) REVERT: L 32 HIS cc_start: 0.8800 (OUTLIER) cc_final: 0.8333 (m-70) REVERT: L 63 LYS cc_start: 0.7619 (tptt) cc_final: 0.7289 (tppt) REVERT: C 56 GLU cc_start: 0.9026 (tp30) cc_final: 0.8647 (tp30) REVERT: C 63 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9158 (mm) REVERT: C 73 ASN cc_start: 0.9370 (t0) cc_final: 0.9072 (t0) REVERT: C 90 ASP cc_start: 0.8539 (t70) cc_final: 0.8192 (t0) REVERT: G 91 GLU cc_start: 0.8213 (pm20) cc_final: 0.7915 (pm20) outliers start: 38 outliers final: 25 residues processed: 308 average time/residue: 0.1373 time to fit residues: 58.7537 Evaluate side-chains 304 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 277 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 60 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 69 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.079437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.055271 restraints weight = 88145.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.056987 restraints weight = 39933.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.058147 restraints weight = 25518.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.058884 restraints weight = 19766.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.059200 restraints weight = 17073.222| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14865 Z= 0.219 Angle : 0.775 11.803 21349 Z= 0.424 Chirality : 0.046 0.284 2418 Planarity : 0.005 0.074 1690 Dihedral : 30.286 159.551 4321 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.08 % Allowed : 25.64 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.26), residues: 987 helix: 1.17 (0.20), residues: 630 sheet: -0.08 (1.11), residues: 24 loop : -1.24 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG F 67 TYR 0.054 0.003 TYR B 88 PHE 0.017 0.002 PHE A 104 TRP 0.019 0.002 TRP K 77 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.22 (14855) covalent geometry : angle 0.76316 / 0.42 (21334) hydrogen bonds : bond 0.05330 / 3.57 ( 844) hydrogen bonds : angle 3.92433 / 2.83 ( 2154) metal coordination : bond 0.01950 / 0.96 ( 8) metal coordination : angle 6.63739 / 2.93 ( 9) link_TRANS : bond 0.00191 / 0.09 ( 2) link_TRANS : angle 0.35568 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 281 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8664 (tmm-80) cc_final: 0.8141 (tmm-80) REVERT: D 33 ARG cc_start: 0.8819 (ttm110) cc_final: 0.8492 (tpp80) REVERT: E 120 MET cc_start: 0.8829 (mmm) cc_final: 0.8277 (mmm) REVERT: F 39 ARG cc_start: 0.9363 (tpp80) cc_final: 0.9127 (mmt-90) REVERT: F 92 ARG cc_start: 0.8795 (ttp80) cc_final: 0.8171 (ttp80) REVERT: H 47 GLN cc_start: 0.8833 (tt0) cc_final: 0.8515 (tm-30) REVERT: H 116 LYS cc_start: 0.9091 (mmmt) cc_final: 0.8604 (mmtp) REVERT: C 56 GLU cc_start: 0.9049 (tp30) cc_final: 0.8659 (tp30) REVERT: C 63 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9176 (mm) REVERT: C 73 ASN cc_start: 0.9374 (t0) cc_final: 0.9075 (t0) REVERT: C 90 ASP cc_start: 0.8547 (t70) cc_final: 0.8165 (t0) outliers start: 35 outliers final: 30 residues processed: 299 average time/residue: 0.1340 time to fit residues: 55.7659 Evaluate side-chains 304 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 273 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 116 optimal weight: 0.9980 chunk 77 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 16 optimal weight: 0.0670 chunk 51 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.081042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.056298 restraints weight = 106203.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.058271 restraints weight = 43469.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.059607 restraints weight = 26371.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060397 restraints weight = 19797.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.060785 restraints weight = 16815.267| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14865 Z= 0.167 Angle : 0.766 12.365 21349 Z= 0.421 Chirality : 0.045 0.280 2418 Planarity : 0.004 0.048 1690 Dihedral : 30.251 159.300 4321 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.50 % Allowed : 26.22 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.27), residues: 987 helix: 1.14 (0.21), residues: 630 sheet: -0.08 (1.12), residues: 24 loop : -1.21 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 67 TYR 0.061 0.003 TYR B 88 PHE 0.013 0.001 PHE A 104 TRP 0.027 0.003 TRP K 77 HIS 0.005 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (14855) covalent geometry : angle 0.75420 / 0.42 (21334) hydrogen bonds : bond 0.04704 / 3.12 ( 844) hydrogen bonds : angle 3.84139 / 2.77 ( 2154) metal coordination : bond 0.01165 / 0.57 ( 8) metal coordination : angle 6.51378 / 2.76 ( 9) link_TRANS : bond 0.00013 / 0.01 ( 2) link_TRANS : angle 0.25219 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 291 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8640 (tmm-80) cc_final: 0.8100 (tmm-80) REVERT: B 53 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8004 (mt-10) REVERT: D 33 ARG cc_start: 0.8769 (ttm110) cc_final: 0.8497 (tpp80) REVERT: E 73 GLU cc_start: 0.8471 (tt0) cc_final: 0.8203 (mt-10) REVERT: E 120 MET cc_start: 0.8925 (mmm) cc_final: 0.8421 (mmm) REVERT: F 39 ARG cc_start: 0.9345 (tpp80) cc_final: 0.9099 (mmt-90) REVERT: F 92 ARG cc_start: 0.8878 (ttp80) cc_final: 0.8323 (ttp80) REVERT: H 47 GLN cc_start: 0.8797 (tt0) cc_final: 0.8505 (tm-30) REVERT: H 105 GLU cc_start: 0.6866 (pm20) cc_final: 0.6598 (pm20) REVERT: H 116 LYS cc_start: 0.9060 (mmmt) cc_final: 0.8597 (mmtp) REVERT: L 63 LYS cc_start: 0.7836 (tptt) cc_final: 0.7597 (tppt) REVERT: C 56 GLU cc_start: 0.9041 (tp30) cc_final: 0.8654 (tp30) REVERT: C 73 ASN cc_start: 0.9336 (t0) cc_final: 0.9047 (t0) REVERT: C 90 ASP cc_start: 0.8533 (t70) cc_final: 0.8215 (t0) REVERT: G 57 TYR cc_start: 0.8699 (t80) cc_final: 0.8461 (t80) REVERT: G 90 ASP cc_start: 0.8441 (t70) cc_final: 0.8202 (t70) outliers start: 30 outliers final: 23 residues processed: 305 average time/residue: 0.1396 time to fit residues: 59.3156 Evaluate side-chains 302 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 279 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 107 CYS Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.0470 chunk 119 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 60 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 53 optimal weight: 30.0000 chunk 2 optimal weight: 0.6980 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.081454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.056856 restraints weight = 92731.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.058739 restraints weight = 40614.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.060017 restraints weight = 25507.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.060725 restraints weight = 19400.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061076 restraints weight = 16729.779| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14865 Z= 0.164 Angle : 0.768 12.621 21349 Z= 0.420 Chirality : 0.046 0.317 2418 Planarity : 0.004 0.037 1690 Dihedral : 30.222 160.704 4321 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.38 % Allowed : 26.34 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.27), residues: 987 helix: 1.07 (0.21), residues: 630 sheet: -0.02 (1.13), residues: 24 loop : -1.21 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 67 TYR 0.052 0.003 TYR B 88 PHE 0.015 0.001 PHE A 104 TRP 0.025 0.002 TRP K 61 HIS 0.008 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (14855) covalent geometry : angle 0.75709 / 0.42 (21334) hydrogen bonds : bond 0.04664 / 3.13 ( 844) hydrogen bonds : angle 3.85026 / 2.77 ( 2154) metal coordination : bond 0.00947 / 0.46 ( 8) metal coordination : angle 6.49105 / 2.73 ( 9) link_TRANS : bond 0.00019 / 0.01 ( 2) link_TRANS : angle 0.19227 / 0.07 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 285 time to evaluate : 0.324 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 53 ARG cc_start: 0.8654 (tmm-80) cc_final: 0.8118 (tmm-80) REVERT: A 64 LYS cc_start: 0.9119 (tppp) cc_final: 0.8790 (tppp) REVERT: D 33 ARG cc_start: 0.8789 (ttm110) cc_final: 0.8120 (tpp80) REVERT: E 120 MET cc_start: 0.8970 (mmm) cc_final: 0.8392 (mmm) REVERT: F 39 ARG cc_start: 0.9348 (tpp80) cc_final: 0.9101 (mmt-90) REVERT: F 92 ARG cc_start: 0.8850 (ttp80) cc_final: 0.8372 (ttp80) REVERT: H 47 GLN cc_start: 0.8782 (tt0) cc_final: 0.8501 (tm-30) REVERT: H 105 GLU cc_start: 0.6832 (pm20) cc_final: 0.6607 (pm20) REVERT: H 116 LYS cc_start: 0.9062 (mmmt) cc_final: 0.8605 (mmtp) REVERT: K 65 HIS cc_start: 0.8681 (m90) cc_final: 0.8377 (m90) REVERT: L 63 LYS cc_start: 0.7718 (tptt) cc_final: 0.7479 (tppt) REVERT: C 56 GLU cc_start: 0.9046 (tp30) cc_final: 0.8670 (tp30) REVERT: C 63 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9189 (mm) REVERT: C 73 ASN cc_start: 0.9307 (t0) cc_final: 0.9035 (t0) REVERT: C 90 ASP cc_start: 0.8558 (t70) cc_final: 0.8180 (t0) REVERT: G 57 TYR cc_start: 0.8702 (t80) cc_final: 0.8455 (t80) outliers start: 29 outliers final: 25 residues processed: 298 average time/residue: 0.1333 time to fit residues: 55.7696 Evaluate side-chains 298 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 272 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 107 CYS Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 121 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 30.0000 chunk 66 optimal weight: 50.0000 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 84 optimal weight: 0.0570 chunk 89 optimal weight: 6.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN A 108 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.079154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.055294 restraints weight = 69666.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.056923 restraints weight = 35272.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.057959 restraints weight = 23877.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.058601 restraints weight = 19144.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.058883 restraints weight = 16876.775| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14865 Z= 0.242 Angle : 0.817 12.425 21349 Z= 0.443 Chirality : 0.048 0.314 2418 Planarity : 0.005 0.044 1690 Dihedral : 30.398 160.819 4321 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.26 % Allowed : 27.04 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.26), residues: 987 helix: 0.96 (0.20), residues: 627 sheet: 0.06 (1.13), residues: 23 loop : -1.31 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 67 TYR 0.053 0.003 TYR F 88 PHE 0.018 0.002 PHE A 104 TRP 0.024 0.002 TRP K 61 HIS 0.009 0.002 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.24 (14855) covalent geometry : angle 0.80483 / 0.44 (21334) hydrogen bonds : bond 0.05798 / 3.97 ( 844) hydrogen bonds : angle 4.09949 / 2.95 ( 2154) metal coordination : bond 0.02120 / 1.05 ( 8) metal coordination : angle 6.81973 / 3.05 ( 9) link_TRANS : bond 0.00197 / 0.10 ( 2) link_TRANS : angle 0.39218 / 0.14 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2785.89 seconds wall clock time: 48 minutes 47.71 seconds (2927.71 seconds total)