Starting phenix.real_space_refine on Sun Aug 24 08:33:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u14_41801/08_2025/8u14_41801.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u14_41801/08_2025/8u14_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8u14_41801/08_2025/8u14_41801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u14_41801/08_2025/8u14_41801.map" model { file = "/net/cci-nas-00/data/ceres_data/8u14_41801/08_2025/8u14_41801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u14_41801/08_2025/8u14_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-2.0-5787/lib/python3.9/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: 3.44, per 1000 atoms: 0.25 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: 1.22 Conformation dependent library (CDL) restraints added in 472.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.49 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: 2.91 Time building geometry restraints manager: 1.64 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=" C HIS H 49 " pdb=" O HIS H 49 " ideal model delta sigma weight residual 1.249 1.237 0.012 8.50e-03 1.38e+04 1.91e+00 bond pdb=" CB LYS B 59 " pdb=" CG LYS B 59 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.40e+00 bond pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 1.460 1.476 -0.017 1.42e-02 4.96e+03 1.35e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.32e+00 ... (remaining 14850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 20629 1.65 - 3.29: 625 3.29 - 4.94: 58 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=" N GLU F 63 " pdb=" CA GLU F 63 " pdb=" CB GLU F 63 " ideal model delta sigma weight residual 110.39 116.07 -5.68 1.66e+00 3.63e-01 1.17e+01 angle pdb=" CA GLU F 63 " pdb=" CB GLU F 63 " pdb=" CG GLU F 63 " ideal model delta sigma weight residual 114.10 120.81 -6.71 2.00e+00 2.50e-01 1.13e+01 angle pdb=" CB LYS B 59 " pdb=" CG LYS B 59 " pdb=" CD LYS B 59 " ideal model delta sigma weight residual 111.30 118.47 -7.17 2.30e+00 1.89e-01 9.73e+00 angle pdb=" N ARG B 36 " pdb=" CA ARG B 36 " pdb=" CB ARG B 36 " ideal model delta sigma weight residual 110.28 114.90 -4.62 1.55e+00 4.16e-01 8.88e+00 ... (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: 1787 0.034 - 0.069: 477 0.069 - 0.103: 120 0.103 - 0.138: 29 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=" CA GLN E 125 " pdb=" N GLN E 125 " pdb=" C GLN E 125 " pdb=" CB GLN E 125 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.070 Find NCS groups from input model: 0.150 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: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 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 : 0.003 0.040 14865 Z= 0.159 Angle : 0.665 12.911 21349 Z= 0.372 Chirality : 0.035 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 aren 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 covalent geometry : bond 0.00335 (14855) covalent geometry : angle 0.64522 (21334) hydrogen bonds : bond 0.10380 ( 844) hydrogen bonds : angle 4.37418 ( 2154) metal coordination : bond 0.00526 ( 8) metal coordination : angle 7.88243 ( 9) link_TRANS : bond 0.00188 ( 2) link_TRANS : angle 0.84845 ( 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 : 0.435 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 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: 0.8526 (tpt) REVERT: E 73 GLU cc_start: 0.8223 (mt-10) cc_final: 0.8008 (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: 0.8430 (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: 0.8206 (tm-30) REVERT: H 85 LYS cc_start: 0.9364 (mtmm) cc_final: 0.9034 (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: 0.8812 (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: 0.7273 (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: 0.1596 time to fit residues: 77.0459 Evaluate side-chains 279 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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: 6.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3641 r_free = 0.3641 target = 0.081460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.057906 restraints weight = 71492.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.059673 restraints weight = 35380.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.060779 restraints weight = 23654.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.061411 restraints weight = 18767.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.061690 restraints weight = 16544.659| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14865 Z= 0.202 Angle : 0.676 14.253 21349 Z= 0.373 Chirality : 0.038 0.224 2418 Planarity : 0.005 0.035 1690 Dihedral : 29.627 156.701 4321 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.10 % Allowed : 18.30 % Favored : 79.60 % 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 aren not related in a simple way. whole: 0.71 (0.26), residues: 987 helix: 1.35 (0.20), residues: 629 sheet: 0.28 (0.97), residues: 24 loop : -1.21 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 136 TYR 0.026 0.002 TYR F 88 PHE 0.019 0.002 PHE A 104 TRP 0.024 0.003 TRP L 33 HIS 0.008 0.001 HIS K 65 Details of bonding type rmsd covalent geometry : bond 0.00450 (14855) covalent geometry : angle 0.65451 (21334) hydrogen bonds : bond 0.04768 ( 844) hydrogen bonds : angle 3.85666 ( 2154) metal coordination : bond 0.01143 ( 8) metal coordination : angle 8.33575 ( 9) link_TRANS : bond 0.00088 ( 2) link_TRANS : angle 0.24042 ( 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 319 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 301 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8450 (mp10) cc_final: 0.8126 (mp10) REVERT: B 84 MET cc_start: 0.9281 (tpp) cc_final: 0.8696 (tpp) REVERT: B 88 TYR cc_start: 0.9040 (m-10) cc_final: 0.8824 (m-10) REVERT: D 33 ARG cc_start: 0.8684 (ttm-80) cc_final: 0.8111 (tpp80) REVERT: D 79 ARG cc_start: 0.8614 (ttm110) cc_final: 0.8408 (ttm110) REVERT: D 95 GLN cc_start: 0.9058 (tp40) cc_final: 0.8519 (tp40) REVERT: E 77 ASP cc_start: 0.8226 (m-30) cc_final: 0.7967 (m-30) REVERT: E 120 MET cc_start: 0.8746 (mmm) cc_final: 0.8340 (mmm) REVERT: F 31 LYS cc_start: 0.9470 (tttm) cc_final: 0.8961 (tttp) REVERT: F 35 ARG cc_start: 0.9290 (ttm110) cc_final: 0.8920 (ttm110) REVERT: F 84 MET cc_start: 0.8163 (tpp) cc_final: 0.7838 (tpp) REVERT: F 92 ARG cc_start: 0.8778 (ttp80) cc_final: 0.8225 (ttp80) REVERT: H 47 GLN cc_start: 0.8842 (tt0) cc_final: 0.8503 (tm-30) REVERT: H 71 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8428 (tm-30) REVERT: K 86 ARG cc_start: 0.9395 (pmt170) cc_final: 0.9088 (pmt170) REVERT: L 63 LYS cc_start: 0.7661 (tptt) cc_final: 0.7346 (tppt) REVERT: C 73 ASN cc_start: 0.9474 (t0) cc_final: 0.9215 (t0) REVERT: C 90 ASP cc_start: 0.8556 (t70) cc_final: 0.8206 (t0) REVERT: G 104 GLN cc_start: 0.8680 (tt0) cc_final: 0.7844 (tm-30) outliers start: 18 outliers final: 9 residues processed: 309 average time/residue: 0.1531 time to fit residues: 64.9169 Evaluate side-chains 295 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 286 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 90 LEU Chi-restraints excluded: chain D residue 63 ASN 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: 0.8980 chunk 22 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 94 ASN ** G 38 ASN ** 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 = 0.3657 r_free = 0.3657 target = 0.082254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.058673 restraints weight = 78386.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.060506 restraints weight = 36534.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061736 restraints weight = 23715.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.062304 restraints weight = 18443.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.062866 restraints weight = 16224.767| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 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 = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14865 Z= 0.166 Angle : 0.650 12.343 21349 Z= 0.361 Chirality : 0.037 0.176 2418 Planarity : 0.004 0.036 1690 Dihedral : 29.636 156.196 4321 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.80 % Allowed : 20.63 % 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 aren not related in a simple way. whole: 0.79 (0.26), residues: 987 helix: 1.46 (0.20), residues: 629 sheet: 0.40 (1.00), residues: 24 loop : -1.29 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 67 TYR 0.028 0.002 TYR C 57 PHE 0.013 0.001 PHE A 104 TRP 0.018 0.001 TRP K 61 HIS 0.003 0.001 HIS K 83 Details of bonding type rmsd covalent geometry : bond 0.00364 (14855) covalent geometry : angle 0.63248 (21334) hydrogen bonds : bond 0.04220 ( 844) hydrogen bonds : angle 3.69667 ( 2154) metal coordination : bond 0.00800 ( 8) metal coordination : angle 7.38779 ( 9) link_TRANS : bond 0.00044 ( 2) link_TRANS : angle 0.20800 ( 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 329 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 305 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8820 (m-30) cc_final: 0.8446 (m-30) REVERT: A 125 GLN cc_start: 0.8375 (mt0) cc_final: 0.8105 (mp10) REVERT: B 84 MET cc_start: 0.9168 (tpp) cc_final: 0.8669 (tpp) REVERT: B 88 TYR cc_start: 0.8940 (m-10) cc_final: 0.8733 (m-10) REVERT: D 33 ARG cc_start: 0.8673 (ttm-80) cc_final: 0.8196 (tpp80) REVERT: D 79 ARG cc_start: 0.8687 (ttm110) cc_final: 0.8331 (ttm110) REVERT: D 95 GLN cc_start: 0.9041 (tp40) cc_final: 0.8565 (tp40) REVERT: E 73 GLU cc_start: 0.8787 (tt0) cc_final: 0.8463 (tt0) REVERT: E 77 ASP cc_start: 0.8243 (m-30) cc_final: 0.7991 (m-30) REVERT: E 90 MET cc_start: 0.8103 (mmt) cc_final: 0.7752 (mmp) REVERT: E 120 MET cc_start: 0.8915 (mmm) cc_final: 0.8426 (mmm) REVERT: E 126 LEU cc_start: 0.9618 (tt) cc_final: 0.9394 (tp) REVERT: F 31 LYS cc_start: 0.9432 (tttm) cc_final: 0.8797 (tttp) REVERT: F 35 ARG cc_start: 0.9239 (ttm110) cc_final: 0.8818 (ttm110) REVERT: F 39 ARG cc_start: 0.9318 (tpp80) cc_final: 0.8995 (mmt-90) REVERT: F 84 MET cc_start: 0.8092 (tpp) cc_final: 0.7772 (tpp) REVERT: F 92 ARG cc_start: 0.8732 (ttp80) cc_final: 0.8216 (ttp80) REVERT: H 47 GLN cc_start: 0.8791 (tt0) cc_final: 0.8474 (tm-30) REVERT: H 71 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8531 (tm-30) REVERT: L 63 LYS cc_start: 0.7568 (tptt) cc_final: 0.7250 (tppt) REVERT: C 73 ASN cc_start: 0.9438 (t0) cc_final: 0.9164 (t0) REVERT: C 90 ASP cc_start: 0.8541 (t70) cc_final: 0.8193 (t0) REVERT: G 57 TYR cc_start: 0.8715 (t80) cc_final: 0.8513 (t80) REVERT: G 84 GLN cc_start: 0.9142 (tp-100) cc_final: 0.8576 (tp-100) REVERT: G 90 ASP cc_start: 0.8559 (t70) cc_final: 0.8139 (t0) REVERT: G 104 GLN cc_start: 0.8695 (tt0) cc_final: 0.7811 (tm-30) outliers start: 24 outliers final: 18 residues processed: 316 average time/residue: 0.1434 time to fit residues: 63.0873 Evaluate side-chains 304 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 286 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 D residue 63 ASN Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 55 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.079600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.055599 restraints weight = 78112.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.057292 restraints weight = 37176.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.058414 restraints weight = 24307.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.059033 restraints weight = 19102.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.059442 restraints weight = 16764.470| |-----------------------------------------------------------------------------| 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 | |-----------------------------------------------------------------------------| r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14865 Z= 0.258 Angle : 0.699 12.498 21349 Z= 0.386 Chirality : 0.039 0.172 2418 Planarity : 0.004 0.035 1690 Dihedral : 29.829 154.334 4321 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.55 % Allowed : 22.96 % Favored : 72.49 % 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 aren not related in a simple way. whole: 0.73 (0.26), residues: 987 helix: 1.41 (0.20), residues: 629 sheet: 0.25 (1.04), residues: 24 loop : -1.30 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 95 TYR 0.025 0.002 TYR C 57 PHE 0.012 0.002 PHE A 104 TRP 0.017 0.002 TRP K 61 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00577 (14855) covalent geometry : angle 0.67957 (21334) hydrogen bonds : bond 0.05097 ( 844) hydrogen bonds : angle 3.83559 ( 2154) metal coordination : bond 0.02103 ( 8) metal coordination : angle 7.95613 ( 9) link_TRANS : bond 0.00189 ( 2) link_TRANS : angle 0.37112 ( 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 336 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 297 time to evaluate : 0.430 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 50 GLU cc_start: 0.8457 (pp20) cc_final: 0.7716 (pp20) REVERT: A 53 ARG cc_start: 0.8701 (tmm-80) cc_final: 0.8141 (tmm-80) REVERT: A 108 ASN cc_start: 0.9268 (t0) cc_final: 0.9019 (t0) REVERT: A 125 GLN cc_start: 0.8309 (mt0) cc_final: 0.8103 (mp10) REVERT: B 84 MET cc_start: 0.9224 (tpp) cc_final: 0.8708 (tpp) REVERT: B 88 TYR cc_start: 0.8974 (m-10) cc_final: 0.8742 (m-10) REVERT: D 33 ARG cc_start: 0.8738 (ttm-80) cc_final: 0.8248 (tpp80) REVERT: E 73 GLU cc_start: 0.8695 (tt0) cc_final: 0.8468 (tt0) REVERT: E 77 ASP cc_start: 0.8247 (m-30) cc_final: 0.8045 (m-30) REVERT: E 90 MET cc_start: 0.8208 (mmt) cc_final: 0.7846 (mmp) REVERT: E 120 MET cc_start: 0.8962 (mmm) cc_final: 0.8411 (mmm) REVERT: F 31 LYS cc_start: 0.9422 (tttm) cc_final: 0.8804 (tttp) REVERT: F 35 ARG cc_start: 0.9245 (ttm110) cc_final: 0.8842 (ttm110) REVERT: F 39 ARG cc_start: 0.9368 (tpp80) cc_final: 0.9139 (mmt-90) REVERT: F 84 MET cc_start: 0.8229 (tpp) cc_final: 0.7943 (tpp) REVERT: F 88 TYR cc_start: 0.7299 (m-10) cc_final: 0.7082 (m-10) REVERT: F 92 ARG cc_start: 0.8787 (ttp80) cc_final: 0.8272 (ttp80) REVERT: H 47 GLN cc_start: 0.8811 (tt0) cc_final: 0.8525 (tm-30) REVERT: H 85 LYS cc_start: 0.9351 (mtmm) cc_final: 0.9128 (mtmm) REVERT: K 64 TYR cc_start: 0.8463 (t80) cc_final: 0.8163 (t80) REVERT: L 63 LYS cc_start: 0.7636 (tptt) cc_final: 0.7316 (tppt) REVERT: C 73 ASN cc_start: 0.9430 (t0) cc_final: 0.9127 (t0) REVERT: C 90 ASP cc_start: 0.8609 (t70) cc_final: 0.8238 (t0) REVERT: G 104 GLN cc_start: 0.8772 (tt0) cc_final: 0.7781 (tm-30) outliers start: 39 outliers final: 31 residues processed: 312 average time/residue: 0.1525 time to fit residues: 65.3930 Evaluate side-chains 314 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 283 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 109 LEU 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 97 LEU 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 82 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain K residue 74 VAL 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 55 LEU 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 74 LYS Chi-restraints excluded: chain G residue 79 ILE 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: 1.9990 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.080610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.057069 restraints weight = 62807.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.058573 restraints weight = 32739.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.059520 restraints weight = 22592.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.060175 restraints weight = 18374.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.060465 restraints weight = 16292.842| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 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 = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14865 Z= 0.187 Angle : 0.671 11.905 21349 Z= 0.371 Chirality : 0.037 0.172 2418 Planarity : 0.004 0.038 1690 Dihedral : 29.837 153.684 4321 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % 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 aren not related in a simple way. whole: 0.82 (0.27), residues: 987 helix: 1.47 (0.20), residues: 628 sheet: 0.32 (1.10), residues: 24 loop : -1.24 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 79 TYR 0.028 0.002 TYR C 57 PHE 0.012 0.001 PHE A 104 TRP 0.019 0.001 TRP K 61 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00419 (14855) covalent geometry : angle 0.65383 (21334) hydrogen bonds : bond 0.04346 ( 844) hydrogen bonds : angle 3.71759 ( 2154) metal coordination : bond 0.01389 ( 8) metal coordination : angle 7.32115 ( 9) link_TRANS : bond 0.00090 ( 2) link_TRANS : angle 0.26325 ( 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 330 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 300 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9253 (t0) cc_final: 0.9035 (t0) REVERT: B 59 LYS cc_start: 0.9139 (tppt) cc_final: 0.8414 (tptp) REVERT: B 84 MET cc_start: 0.9145 (tpp) cc_final: 0.8659 (tpp) REVERT: B 88 TYR cc_start: 0.8953 (m-10) cc_final: 0.8683 (m-10) REVERT: E 73 GLU cc_start: 0.8688 (tt0) cc_final: 0.8429 (tt0) REVERT: E 77 ASP cc_start: 0.8145 (m-30) cc_final: 0.7926 (m-30) REVERT: E 90 MET cc_start: 0.8205 (mmt) cc_final: 0.7874 (mmp) REVERT: E 120 MET cc_start: 0.8977 (mmm) cc_final: 0.8349 (mmm) REVERT: F 31 LYS cc_start: 0.9402 (tttm) cc_final: 0.8814 (tttp) REVERT: F 35 ARG cc_start: 0.9215 (ttm110) cc_final: 0.8771 (ttm110) REVERT: F 39 ARG cc_start: 0.9341 (tpp80) cc_final: 0.9117 (mmt-90) REVERT: F 92 ARG cc_start: 0.8723 (ttp80) cc_final: 0.8202 (ttp80) REVERT: H 47 GLN cc_start: 0.8795 (tt0) cc_final: 0.8513 (tm-30) REVERT: H 116 LYS cc_start: 0.9078 (mmmt) cc_final: 0.8719 (mmtp) REVERT: K 63 ARG cc_start: 0.8329 (ptm-80) cc_final: 0.7878 (ptm-80) REVERT: K 64 TYR cc_start: 0.8461 (t80) cc_final: 0.8197 (t80) REVERT: L 63 LYS cc_start: 0.7559 (tptt) cc_final: 0.7229 (tppt) REVERT: C 73 ASN cc_start: 0.9376 (t0) cc_final: 0.9070 (t0) REVERT: C 90 ASP cc_start: 0.8578 (t70) cc_final: 0.8203 (t0) REVERT: G 57 TYR cc_start: 0.8755 (t80) cc_final: 0.8504 (t80) REVERT: G 104 GLN cc_start: 0.8715 (tt0) cc_final: 0.7762 (tm-30) outliers start: 30 outliers final: 24 residues processed: 310 average time/residue: 0.1534 time to fit residues: 65.1134 Evaluate side-chains 311 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 287 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 97 LEU 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 96 CYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 94 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.081291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.057206 restraints weight = 74428.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.058981 restraints weight = 35977.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.059999 restraints weight = 23697.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.060679 restraints weight = 18720.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061009 restraints weight = 16496.600| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14865 Z= 0.174 Angle : 0.678 11.891 21349 Z= 0.372 Chirality : 0.037 0.205 2418 Planarity : 0.004 0.047 1690 Dihedral : 29.812 154.548 4321 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.96 % Allowed : 26.22 % Favored : 69.81 % 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 aren not related in a simple way. whole: 0.81 (0.27), residues: 987 helix: 1.48 (0.20), residues: 624 sheet: 0.18 (0.96), residues: 29 loop : -1.24 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 67 TYR 0.022 0.002 TYR C 57 PHE 0.012 0.001 PHE A 104 TRP 0.020 0.002 TRP K 61 HIS 0.003 0.001 HIS K 83 Details of bonding type rmsd covalent geometry : bond 0.00389 (14855) covalent geometry : angle 0.66122 (21334) hydrogen bonds : bond 0.04213 ( 844) hydrogen bonds : angle 3.67602 ( 2154) metal coordination : bond 0.01138 ( 8) metal coordination : angle 7.28833 ( 9) link_TRANS : bond 0.00051 ( 2) link_TRANS : angle 0.20864 ( 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 330 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 296 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 50 GLU cc_start: 0.8439 (pp20) cc_final: 0.7623 (pp20) REVERT: A 53 ARG cc_start: 0.8715 (tmm-80) cc_final: 0.8149 (tmm-80) REVERT: B 84 MET cc_start: 0.9101 (tpp) cc_final: 0.8660 (tpp) REVERT: B 88 TYR cc_start: 0.8894 (m-10) cc_final: 0.8607 (m-10) REVERT: E 90 MET cc_start: 0.8162 (mmt) cc_final: 0.7836 (mmp) REVERT: E 120 MET cc_start: 0.8956 (mmm) cc_final: 0.8284 (mmm) REVERT: F 31 LYS cc_start: 0.9427 (tttm) cc_final: 0.8892 (tttp) REVERT: F 35 ARG cc_start: 0.9221 (ttm110) cc_final: 0.8796 (ttm110) REVERT: F 39 ARG cc_start: 0.9346 (tpp80) cc_final: 0.9124 (mmt-90) REVERT: F 84 MET cc_start: 0.8195 (tpp) cc_final: 0.7820 (tpp) REVERT: F 92 ARG cc_start: 0.8758 (ttp80) cc_final: 0.8254 (ttp80) REVERT: H 47 GLN cc_start: 0.8788 (tt0) cc_final: 0.8485 (tm-30) REVERT: H 71 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8445 (tm-30) REVERT: K 64 TYR cc_start: 0.8522 (t80) cc_final: 0.8243 (t80) REVERT: L 32 HIS cc_start: 0.8663 (OUTLIER) cc_final: 0.8194 (m-70) REVERT: L 63 LYS cc_start: 0.7562 (tptt) cc_final: 0.7226 (tppt) REVERT: C 73 ASN cc_start: 0.9355 (t0) cc_final: 0.9043 (t0) REVERT: C 90 ASP cc_start: 0.8558 (t70) cc_final: 0.8188 (t0) REVERT: G 57 TYR cc_start: 0.8759 (t80) cc_final: 0.8512 (t80) outliers start: 34 outliers final: 26 residues processed: 309 average time/residue: 0.1277 time to fit residues: 54.5272 Evaluate side-chains 306 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 279 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU 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 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU 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 94 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 96 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 90 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 108 ASN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.080951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.056487 restraints weight = 105492.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.058426 restraints weight = 42728.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.059737 restraints weight = 25895.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060502 restraints weight = 19269.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061034 restraints weight = 16352.732| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 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 = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14865 Z= 0.186 Angle : 0.696 13.700 21349 Z= 0.381 Chirality : 0.038 0.191 2418 Planarity : 0.004 0.039 1690 Dihedral : 29.847 154.404 4321 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.96 % Allowed : 27.51 % Favored : 68.53 % 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 aren not related in a simple way. whole: 0.76 (0.27), residues: 987 helix: 1.40 (0.21), residues: 626 sheet: 0.18 (0.94), residues: 29 loop : -1.20 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 63 TYR 0.020 0.002 TYR C 57 PHE 0.012 0.001 PHE A 104 TRP 0.022 0.002 TRP K 61 HIS 0.008 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00417 (14855) covalent geometry : angle 0.68125 (21334) hydrogen bonds : bond 0.04334 ( 844) hydrogen bonds : angle 3.73148 ( 2154) metal coordination : bond 0.01294 ( 8) metal coordination : angle 7.01129 ( 9) link_TRANS : bond 0.00061 ( 2) link_TRANS : angle 0.22479 ( 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 321 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 287 time to evaluate : 0.339 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: B 59 LYS cc_start: 0.9142 (tppt) cc_final: 0.8430 (tptp) REVERT: B 84 MET cc_start: 0.9101 (tpp) cc_final: 0.8667 (tpp) REVERT: B 88 TYR cc_start: 0.8915 (m-10) cc_final: 0.8627 (m-10) REVERT: E 90 MET cc_start: 0.8070 (mmt) cc_final: 0.7764 (mmp) REVERT: E 120 MET cc_start: 0.8971 (mmm) cc_final: 0.8278 (mmm) REVERT: E 125 GLN cc_start: 0.9339 (OUTLIER) cc_final: 0.9107 (mp10) REVERT: F 39 ARG cc_start: 0.9343 (tpp80) cc_final: 0.9116 (mmt-90) REVERT: F 77 LYS cc_start: 0.9115 (mmtm) cc_final: 0.8869 (mmtm) REVERT: F 84 MET cc_start: 0.8174 (tpp) cc_final: 0.7887 (tpp) REVERT: F 92 ARG cc_start: 0.8760 (ttp80) cc_final: 0.8300 (ttp80) REVERT: H 47 GLN cc_start: 0.8804 (tt0) cc_final: 0.8549 (tm-30) REVERT: H 71 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8449 (tm-30) REVERT: K 64 TYR cc_start: 0.8518 (t80) cc_final: 0.8273 (t80) REVERT: L 32 HIS cc_start: 0.8659 (OUTLIER) cc_final: 0.8144 (m-70) REVERT: C 73 ASN cc_start: 0.9355 (t0) cc_final: 0.9047 (t0) REVERT: C 90 ASP cc_start: 0.8551 (t70) cc_final: 0.8174 (t0) REVERT: G 57 TYR cc_start: 0.8764 (t80) cc_final: 0.8505 (t80) outliers start: 34 outliers final: 28 residues processed: 305 average time/residue: 0.1351 time to fit residues: 57.0354 Evaluate side-chains 306 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 276 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 B residue 96 THR Chi-restraints excluded: chain D residue 67 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 E residue 125 GLN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU 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 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: 3.9990 chunk 94 optimal weight: 40.0000 chunk 28 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 102 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.079772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.055775 restraints weight = 86896.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.057464 restraints weight = 38728.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.058660 restraints weight = 24638.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.059444 restraints weight = 18906.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.059774 restraints weight = 16223.781| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 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 = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14865 Z= 0.219 Angle : 0.718 13.619 21349 Z= 0.392 Chirality : 0.039 0.242 2418 Planarity : 0.004 0.039 1690 Dihedral : 30.011 152.933 4321 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.96 % Allowed : 27.39 % Favored : 68.65 % 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 aren not related in a simple way. whole: 0.62 (0.26), residues: 987 helix: 1.31 (0.20), residues: 626 sheet: 0.23 (0.93), residues: 28 loop : -1.29 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 79 TYR 0.020 0.002 TYR G 39 PHE 0.018 0.001 PHE A 104 TRP 0.024 0.002 TRP K 77 HIS 0.006 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00493 (14855) covalent geometry : angle 0.70291 (21334) hydrogen bonds : bond 0.04758 ( 844) hydrogen bonds : angle 3.79994 ( 2154) metal coordination : bond 0.01958 ( 8) metal coordination : angle 7.19835 ( 9) link_TRANS : bond 0.00120 ( 2) link_TRANS : angle 0.29630 ( 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 321 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 287 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8752 (tmm-80) cc_final: 0.8194 (tmm-80) REVERT: B 84 MET cc_start: 0.9075 (tpp) cc_final: 0.8348 (tpp) REVERT: D 67 ASN cc_start: 0.8838 (OUTLIER) cc_final: 0.8631 (t0) REVERT: E 73 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7582 (mt-10) REVERT: E 77 ASP cc_start: 0.8227 (m-30) cc_final: 0.7998 (m-30) REVERT: E 90 MET cc_start: 0.8093 (mmt) cc_final: 0.7774 (mmp) REVERT: E 120 MET cc_start: 0.9014 (mmm) cc_final: 0.8300 (mmm) REVERT: E 125 GLN cc_start: 0.9327 (OUTLIER) cc_final: 0.9100 (mp10) REVERT: F 39 ARG cc_start: 0.9343 (tpp80) cc_final: 0.9115 (mmt-90) REVERT: F 77 LYS cc_start: 0.9090 (mmtm) cc_final: 0.8815 (mmtm) REVERT: F 84 MET cc_start: 0.8242 (tpp) cc_final: 0.7986 (tpp) REVERT: F 92 ARG cc_start: 0.8753 (ttp80) cc_final: 0.8217 (ttp80) REVERT: H 47 GLN cc_start: 0.8791 (tt0) cc_final: 0.8513 (tm-30) REVERT: H 71 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8488 (tm-30) REVERT: K 64 TYR cc_start: 0.8547 (t80) cc_final: 0.8307 (t80) REVERT: L 63 LYS cc_start: 0.7671 (tptt) cc_final: 0.7341 (tppt) REVERT: C 73 ASN cc_start: 0.9369 (t0) cc_final: 0.9058 (t0) REVERT: C 90 ASP cc_start: 0.8589 (t70) cc_final: 0.8237 (t0) REVERT: G 57 TYR cc_start: 0.8771 (t80) cc_final: 0.8530 (t80) REVERT: G 91 GLU cc_start: 0.8372 (pp20) cc_final: 0.7915 (pp20) outliers start: 34 outliers final: 28 residues processed: 303 average time/residue: 0.1311 time to fit residues: 55.2270 Evaluate side-chains 307 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 277 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 B residue 97 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 13 SER 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 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 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: 2.9990 chunk 77 optimal weight: 7.9990 chunk 35 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 102 optimal weight: 0.0170 chunk 74 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 overall best weight: 0.9024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.081851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.057103 restraints weight = 106165.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.059094 restraints weight = 43383.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.060406 restraints weight = 26211.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061194 restraints weight = 19652.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.061727 restraints weight = 16664.007| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 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 = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14865 Z= 0.169 Angle : 0.719 13.506 21349 Z= 0.392 Chirality : 0.038 0.211 2418 Planarity : 0.004 0.040 1690 Dihedral : 29.914 154.096 4321 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.38 % Allowed : 28.90 % Favored : 67.72 % 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 aren not related in a simple way. whole: 0.62 (0.27), residues: 987 helix: 1.27 (0.20), residues: 630 sheet: 0.19 (0.93), residues: 29 loop : -1.23 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 63 TYR 0.032 0.002 TYR D 83 PHE 0.016 0.001 PHE A 104 TRP 0.021 0.002 TRP K 61 HIS 0.005 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00377 (14855) covalent geometry : angle 0.70544 (21334) hydrogen bonds : bond 0.04158 ( 844) hydrogen bonds : angle 3.71101 ( 2154) metal coordination : bond 0.00873 ( 8) metal coordination : angle 6.84435 ( 9) link_TRANS : bond 0.00025 ( 2) link_TRANS : angle 0.14949 ( 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 317 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 288 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8713 (tmm-80) cc_final: 0.8179 (tmm-80) REVERT: B 59 LYS cc_start: 0.8975 (tppt) cc_final: 0.8302 (tptp) REVERT: B 84 MET cc_start: 0.9023 (tpp) cc_final: 0.8708 (tpp) REVERT: E 73 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7680 (mt-10) REVERT: E 77 ASP cc_start: 0.8193 (m-30) cc_final: 0.7977 (m-30) REVERT: E 90 MET cc_start: 0.8078 (mmt) cc_final: 0.7753 (mmp) REVERT: E 120 MET cc_start: 0.9000 (mmm) cc_final: 0.8288 (mmm) REVERT: F 39 ARG cc_start: 0.9336 (tpp80) cc_final: 0.9090 (mmt-90) REVERT: F 77 LYS cc_start: 0.9080 (mmtm) cc_final: 0.8789 (mmtm) REVERT: F 84 MET cc_start: 0.8283 (tpp) cc_final: 0.8002 (tpp) REVERT: F 92 ARG cc_start: 0.8804 (ttp80) cc_final: 0.8402 (ttp80) REVERT: H 47 GLN cc_start: 0.8758 (tt0) cc_final: 0.8496 (tm-30) REVERT: H 71 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8487 (tm-30) REVERT: K 64 TYR cc_start: 0.8437 (t80) cc_final: 0.8183 (t80) REVERT: L 63 LYS cc_start: 0.7618 (tptt) cc_final: 0.7364 (tppt) REVERT: C 36 LYS cc_start: 0.9253 (pttt) cc_final: 0.9015 (ptmm) REVERT: C 63 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9230 (mm) REVERT: C 73 ASN cc_start: 0.9339 (t0) cc_final: 0.9037 (t0) REVERT: C 90 ASP cc_start: 0.8554 (t70) cc_final: 0.8179 (t0) REVERT: G 57 TYR cc_start: 0.8711 (t80) cc_final: 0.8484 (t80) REVERT: G 90 ASP cc_start: 0.8657 (t70) cc_final: 0.8381 (t0) outliers start: 29 outliers final: 22 residues processed: 300 average time/residue: 0.1222 time to fit residues: 51.0343 Evaluate side-chains 303 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 280 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 B residue 97 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 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 86 LEU Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 63 LEU 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 103 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.080591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.056215 restraints weight = 93208.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.058050 restraints weight = 40819.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.059294 restraints weight = 25521.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.060016 restraints weight = 19461.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.060460 restraints weight = 16762.234| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 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 = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14865 Z= 0.204 Angle : 0.747 13.696 21349 Z= 0.404 Chirality : 0.039 0.306 2418 Planarity : 0.005 0.049 1690 Dihedral : 29.958 154.306 4321 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.38 % Allowed : 29.95 % Favored : 66.67 % 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 aren not related in a simple way. whole: 0.58 (0.26), residues: 987 helix: 1.25 (0.20), residues: 628 sheet: 0.33 (0.93), residues: 28 loop : -1.28 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 63 TYR 0.056 0.002 TYR D 83 PHE 0.015 0.001 PHE A 104 TRP 0.023 0.002 TRP K 61 HIS 0.005 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00462 (14855) covalent geometry : angle 0.73349 (21334) hydrogen bonds : bond 0.04552 ( 844) hydrogen bonds : angle 3.83928 ( 2154) metal coordination : bond 0.01405 ( 8) metal coordination : angle 6.89152 ( 9) link_TRANS : bond 0.00091 ( 2) link_TRANS : angle 0.21115 ( 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 311 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 282 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.7800 (m-80) cc_final: 0.7445 (m-80) REVERT: B 59 LYS cc_start: 0.9035 (tppt) cc_final: 0.8342 (tptp) REVERT: B 84 MET cc_start: 0.9064 (tpp) cc_final: 0.8748 (tpp) REVERT: E 73 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7523 (mt-10) REVERT: E 77 ASP cc_start: 0.8227 (m-30) cc_final: 0.8021 (m-30) REVERT: E 90 MET cc_start: 0.8098 (mmt) cc_final: 0.7779 (mmp) REVERT: E 120 MET cc_start: 0.8995 (mmm) cc_final: 0.8295 (mmm) REVERT: F 39 ARG cc_start: 0.9337 (tpp80) cc_final: 0.9104 (mmt-90) REVERT: F 77 LYS cc_start: 0.9097 (mmtm) cc_final: 0.8807 (mmtm) REVERT: F 92 ARG cc_start: 0.8839 (ttp80) cc_final: 0.8377 (ttp80) REVERT: H 47 GLN cc_start: 0.8719 (tt0) cc_final: 0.8484 (tm-30) REVERT: H 71 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8499 (tm-30) REVERT: K 63 ARG cc_start: 0.8573 (ptm-80) cc_final: 0.8282 (ptm-80) REVERT: K 64 TYR cc_start: 0.8444 (t80) cc_final: 0.8194 (t80) REVERT: L 63 LYS cc_start: 0.7596 (tptt) cc_final: 0.7345 (tppt) REVERT: C 36 LYS cc_start: 0.9253 (pttt) cc_final: 0.9027 (ptmm) REVERT: C 63 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9206 (mm) REVERT: C 90 ASP cc_start: 0.8436 (t70) cc_final: 0.7995 (t0) REVERT: C 95 LYS cc_start: 0.9276 (tmtt) cc_final: 0.9069 (pttp) REVERT: G 57 TYR cc_start: 0.8753 (t80) cc_final: 0.8525 (t80) REVERT: G 90 ASP cc_start: 0.8599 (t70) cc_final: 0.7959 (t0) outliers start: 29 outliers final: 24 residues processed: 295 average time/residue: 0.1335 time to fit residues: 54.6997 Evaluate side-chains 302 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 277 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 D residue 98 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 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 54 ILE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 63 LEU 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 79 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: 10.0000 chunk 100 optimal weight: 20.0000 chunk 23 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS E 68 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 68 ASN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.082056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.058303 restraints weight = 68069.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.059992 restraints weight = 33990.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.061080 restraints weight = 22793.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.061711 restraints weight = 18110.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.061926 restraints weight = 15880.631| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 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 = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14865 Z= 0.172 Angle : 0.752 13.321 21349 Z= 0.405 Chirality : 0.039 0.294 2418 Planarity : 0.004 0.051 1690 Dihedral : 29.905 154.214 4321 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.56 % Allowed : 30.65 % Favored : 66.78 % 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 aren not related in a simple way. whole: 0.54 (0.26), residues: 987 helix: 1.20 (0.20), residues: 628 sheet: 0.55 (0.94), residues: 28 loop : -1.28 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 63 TYR 0.042 0.002 TYR D 83 PHE 0.018 0.002 PHE A 104 TRP 0.023 0.002 TRP K 61 HIS 0.005 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00384 (14855) covalent geometry : angle 0.73953 (21334) hydrogen bonds : bond 0.04245 ( 844) hydrogen bonds : angle 3.86780 ( 2154) metal coordination : bond 0.00763 ( 8) metal coordination : angle 6.64915 ( 9) link_TRANS : bond 0.00017 ( 2) link_TRANS : angle 0.11605 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2955.20 seconds wall clock time: 51 minutes 27.67 seconds (3087.67 seconds total)