Starting phenix.real_space_refine on Sat Jul 4 04:45:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8u14_41801/07_2026/8u14_41801.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u14_41801/07_2026/8u14_41801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8u14_41801/07_2026/8u14_41801.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8u14_41801/07_2026/8u14_41801.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u14_41801/07_2026/8u14_41801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u14_41801/07_2026/8u14_41801.map" model { file = "/net/cci-nas-00/data/ceres_data/8u14_41801/07_2026/8u14_41801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u14_41801/07_2026/8u14_41801.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 293 5.49 5 S 32 5.16 5 C 7885 2.51 5 N 2608 2.21 5 O 3175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13995 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 751 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 706 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Conformer: "B" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} bond proxies already assigned to first conformer: 713 Chain: "L" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1176 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "C" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 843 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10611 SG CYS K 31 77.501 68.587 45.284 1.00155.98 S ATOM 10761 SG CYS K 51 77.762 71.763 47.414 1.00157.25 S ATOM 10785 SG CYS K 54 76.542 71.999 43.785 1.00157.66 S ATOM 10502 SG CYS K 16 86.876 72.181 56.653 1.00201.51 S ATOM 10520 SG CYS K 19 87.004 73.675 59.834 1.00219.51 S ATOM 10650 SG CYS K 36 84.987 70.188 59.204 1.00192.64 S ATOM 10672 SG CYS K 39 83.453 73.315 58.539 1.00199.41 S Time building chain proxies: 3.01, per 1000 atoms: 0.22 Number of scatterers: 13995 At special positions: 0 Unit cell: (107.898, 126.395, 118.174, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 32 16.00 P 293 15.00 O 3175 8.00 N 2608 7.00 C 7885 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 456.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " Number of angles added : 9 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 8 sheets defined 65.5% alpha, 3.3% beta 140 base pairs and 241 stacking pairs defined. Time for finding SS restraints: 1.83 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: 2.57 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3398 1.34 - 1.46: 4244 1.46 - 1.58: 6583 1.58 - 1.70: 584 1.70 - 1.82: 46 Bond restraints: 14855 Sorted by residual: bond pdb=" C3' DT J 13 " pdb=" C2' DT J 13 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DT J -57 " pdb=" C2' DT J -57 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DG I 40 " pdb=" C2' DG I 40 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DC I -18 " pdb=" C2' DC I -18 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 14850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 20084 1.65 - 3.29: 1160 3.29 - 4.94: 68 4.94 - 6.59: 16 6.59 - 8.23: 6 Bond angle restraints: 21334 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 113.53 108.56 4.97 9.80e-01 1.04e+00 2.57e+01 angle pdb=" O4' DT I -26 " pdb=" C4' DT I -26 " pdb=" C3' DT I -26 " ideal model delta sigma weight residual 106.00 103.31 2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT J -17 " pdb=" C4 DT J -17 " pdb=" O4 DT J -17 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" O4' DG J -49 " pdb=" C4' DG J -49 " pdb=" C3' DG J -49 " ideal model delta sigma weight residual 106.00 103.42 2.58 6.00e-01 2.78e+00 1.84e+01 ... (remaining 21329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.61: 6645 31.61 - 63.22: 1529 63.22 - 94.84: 42 94.84 - 126.45: 0 126.45 - 158.06: 2 Dihedral angle restraints: 8218 sinusoidal: 5288 harmonic: 2930 Sorted by residual: dihedral pdb=" CA ASN B 25 " pdb=" C ASN B 25 " pdb=" N ILE B 26 " pdb=" CA ILE B 26 " ideal model delta harmonic sigma weight residual 180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 61.94 158.06 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 65.92 154.08 1 3.50e+01 8.16e-04 1.49e+01 ... (remaining 8215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1452 0.034 - 0.069: 662 0.069 - 0.103: 238 0.103 - 0.138: 61 0.138 - 0.172: 5 Chirality restraints: 2418 Sorted by residual: chirality pdb=" CA GLU F 63 " pdb=" N GLU F 63 " pdb=" C GLU F 63 " pdb=" CB GLU F 63 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" P DT J -16 " pdb=" OP1 DT J -16 " pdb=" OP2 DT J -16 " pdb=" O5' DT J -16 " both_signs ideal model delta sigma weight residual True 2.34 -2.48 -0.15 2.00e-01 2.50e+01 5.51e-01 ... (remaining 2415 not shown) Planarity restraints: 1692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.024 2.00e-02 2.50e+03 1.04e-02 2.98e+00 pdb=" N9 DA I -35 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C LYS F 59 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS F 59 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL F 60 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 73 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" CD GLU A 73 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU A 73 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A 73 " -0.010 2.00e-02 2.50e+03 ... (remaining 1689 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 466 2.68 - 3.23: 13143 3.23 - 3.79: 27192 3.79 - 4.34: 32816 4.34 - 4.90: 46740 Nonbonded interactions: 120357 Sorted by model distance: nonbonded pdb=" O ARG K 63 " pdb=" NH1 ARG K 67 " model vdw 2.124 3.120 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.150 2.496 nonbonded pdb=" OE1 GLN D 95 " pdb=" OH TYR C 50 " model vdw 2.160 3.040 nonbonded pdb=" NE2 HIS B 75 " pdb=" OE1 GLU D 93 " model vdw 2.204 3.120 nonbonded pdb=" OE2 GLU H 105 " pdb=" NH1 ARG K 67 " model vdw 2.223 3.120 ... (remaining 120352 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 119) } ncs_group { reference = (chain 'D' and resid 31 through 123) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.230 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14865 Z= 0.482 Angle : 0.795 12.911 21349 Z= 0.641 Chirality : 0.044 0.172 2418 Planarity : 0.004 0.041 1690 Dihedral : 26.360 158.059 6320 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.27), residues: 987 helix: 1.25 (0.21), residues: 623 sheet: 0.72 (0.98), residues: 24 loop : -1.10 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 36 TYR 0.024 0.001 TYR F 88 PHE 0.017 0.001 PHE E 78 TRP 0.011 0.001 TRP K 61 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.48 (14855) covalent geometry : angle 0.77865 / 0.64 (21334) hydrogen bonds : bond 0.10380 / 6.51 ( 844) hydrogen bonds : angle 4.37418 / 3.14 ( 2154) metal coordination : bond 0.00526 / 0.30 ( 8) metal coordination : angle 7.88243 / 3.35 ( 9) link_TRANS : bond 0.00188 / 0.09 ( 2) link_TRANS : angle 0.84845 / 0.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.1366 time to fit residues: 66.7096 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 : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 40.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 76 GLN E 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.081498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.058069 restraints weight = 66997.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.059751 restraints weight = 34203.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.060816 restraints weight = 23256.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.061441 restraints weight = 18638.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061716 restraints weight = 16485.198| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 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 = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14865 Z= 0.200 Angle : 0.743 15.752 21349 Z= 0.416 Chirality : 0.046 0.223 2418 Planarity : 0.005 0.059 1690 Dihedral : 29.895 160.576 4321 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.45 % Allowed : 17.37 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.26), residues: 987 helix: 1.25 (0.21), residues: 630 sheet: 0.38 (0.99), residues: 24 loop : -1.32 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 86 TYR 0.030 0.002 TYR F 88 PHE 0.019 0.002 PHE A 104 TRP 0.018 0.002 TRP K 61 HIS 0.005 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.20 (14855) covalent geometry : angle 0.71988 / 0.41 (21334) hydrogen bonds : bond 0.05498 / 3.60 ( 844) hydrogen bonds : angle 3.99468 / 2.91 ( 2154) metal coordination : bond 0.00744 / 0.35 ( 8) metal coordination : angle 8.90569 / 3.79 ( 9) link_TRANS : bond 0.00075 / 0.04 ( 2) link_TRANS : angle 0.60615 / 0.22 ( 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 324 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 303 time to evaluate : 0.297 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: 0.8935 (tmm-80) cc_final: 0.8724 (tmm-80) REVERT: A 106 ASP cc_start: 0.8968 (m-30) cc_final: 0.8688 (m-30) REVERT: A 125 GLN cc_start: 0.8524 (mp10) cc_final: 0.8165 (mp10) REVERT: B 84 MET cc_start: 0.9293 (tpp) cc_final: 0.8943 (tpp) REVERT: D 33 ARG cc_start: 0.8628 (ttm-80) cc_final: 0.8130 (tpp80) REVERT: D 95 GLN cc_start: 0.9061 (tp40) cc_final: 0.8462 (tp40) REVERT: E 120 MET cc_start: 0.8749 (mmm) cc_final: 0.8342 (mmm) REVERT: F 27 GLN cc_start: 0.9226 (mp10) cc_final: 0.8992 (mp10) REVERT: F 84 MET cc_start: 0.8187 (tpp) cc_final: 0.7929 (tpp) REVERT: H 47 GLN cc_start: 0.8850 (tt0) cc_final: 0.8506 (tm-30) REVERT: H 71 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8428 (tm-30) REVERT: K 63 ARG cc_start: 0.8593 (ptm-80) cc_final: 0.8218 (ptm-80) REVERT: K 86 ARG cc_start: 0.9330 (pmt170) cc_final: 0.9053 (pmt170) REVERT: C 56 GLU cc_start: 0.9102 (tp30) cc_final: 0.8807 (tp30) REVERT: C 73 ASN cc_start: 0.9497 (t0) cc_final: 0.9227 (t0) REVERT: C 90 ASP cc_start: 0.8550 (t70) cc_final: 0.8210 (t0) REVERT: G 38 ASN cc_start: 0.8014 (m110) cc_final: 0.7327 (m-40) REVERT: G 90 ASP cc_start: 0.8586 (t70) cc_final: 0.8143 (t70) REVERT: G 104 GLN cc_start: 0.8668 (tt0) cc_final: 0.7868 (tm-30) outliers start: 21 outliers final: 12 residues processed: 311 average time/residue: 0.1251 time to fit residues: 53.9245 Evaluate side-chains 295 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 283 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 46 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.082178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.058209 restraints weight = 78278.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.060077 restraints weight = 36688.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061229 restraints weight = 23811.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.061976 restraints weight = 18554.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.062297 restraints weight = 16117.293| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14865 Z= 0.159 Angle : 0.695 12.061 21349 Z= 0.395 Chirality : 0.044 0.249 2418 Planarity : 0.005 0.038 1690 Dihedral : 29.978 159.896 4321 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.91 % Allowed : 20.51 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.26), residues: 987 helix: 1.32 (0.20), residues: 629 sheet: 0.29 (1.02), residues: 24 loop : -1.31 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 79 TYR 0.031 0.002 TYR B 88 PHE 0.014 0.002 PHE A 104 TRP 0.012 0.001 TRP K 61 HIS 0.004 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 (14855) covalent geometry : angle 0.67814 / 0.39 (21334) hydrogen bonds : bond 0.04803 / 3.11 ( 844) hydrogen bonds : angle 3.82189 / 2.79 ( 2154) metal coordination : bond 0.00721 / 0.35 ( 8) metal coordination : angle 7.37051 / 3.13 ( 9) link_TRANS : bond 0.00029 / 0.01 ( 2) link_TRANS : angle 0.12662 / 0.05 ( 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 323 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 298 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8437 (mp10) cc_final: 0.8075 (mp10) REVERT: E 73 GLU cc_start: 0.8801 (tt0) cc_final: 0.8504 (tt0) REVERT: E 77 ASP cc_start: 0.8240 (m-30) cc_final: 0.8003 (m-30) REVERT: E 120 MET cc_start: 0.8772 (mmm) cc_final: 0.8300 (mmm) REVERT: F 39 ARG cc_start: 0.9332 (tpp80) cc_final: 0.8990 (mmt-90) REVERT: F 64 ASN cc_start: 0.8624 (m-40) cc_final: 0.8297 (m110) REVERT: F 84 MET cc_start: 0.8075 (tpp) cc_final: 0.7797 (tpp) REVERT: F 92 ARG cc_start: 0.8653 (ttp80) cc_final: 0.8188 (ttp80) REVERT: H 47 GLN cc_start: 0.8798 (tt0) cc_final: 0.8490 (tm-30) REVERT: H 71 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8506 (tm-30) REVERT: H 85 LYS cc_start: 0.9340 (mtmm) cc_final: 0.9124 (mtmm) REVERT: H 93 GLU cc_start: 0.8840 (mp0) cc_final: 0.8608 (mp0) REVERT: H 116 LYS cc_start: 0.9099 (mmtt) cc_final: 0.8640 (mmtp) REVERT: K 68 ARG cc_start: 0.6807 (mpp-170) cc_final: 0.6287 (mpp80) REVERT: K 86 ARG cc_start: 0.9385 (pmt170) cc_final: 0.9168 (pmt170) REVERT: L 32 HIS cc_start: 0.8844 (OUTLIER) cc_final: 0.8330 (m-70) REVERT: L 63 LYS cc_start: 0.7518 (tptt) cc_final: 0.7190 (tppt) REVERT: C 56 GLU cc_start: 0.9067 (tp30) cc_final: 0.8686 (tp30) REVERT: C 73 ASN cc_start: 0.9487 (t0) cc_final: 0.9228 (t0) REVERT: C 90 ASP cc_start: 0.8511 (t70) cc_final: 0.8159 (t0) REVERT: G 57 TYR cc_start: 0.8707 (t80) cc_final: 0.8505 (t80) REVERT: G 90 ASP cc_start: 0.8494 (t70) cc_final: 0.8045 (t70) REVERT: G 104 GLN cc_start: 0.8710 (tt0) cc_final: 0.7845 (tm-30) outliers start: 25 outliers final: 18 residues processed: 307 average time/residue: 0.1383 time to fit residues: 59.3960 Evaluate side-chains 298 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 279 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 55 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 chunk 83 optimal weight: 0.0270 chunk 68 optimal weight: 20.0000 chunk 23 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.081999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.058387 restraints weight = 78404.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.060141 restraints weight = 36592.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061378 restraints weight = 23769.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.062090 restraints weight = 18454.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.062443 restraints weight = 16000.507| |-----------------------------------------------------------------------------| 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14865 Z= 0.165 Angle : 0.692 11.273 21349 Z= 0.392 Chirality : 0.043 0.264 2418 Planarity : 0.004 0.042 1690 Dihedral : 30.058 160.978 4321 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.26 % Allowed : 22.84 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.27), residues: 987 helix: 1.36 (0.21), residues: 629 sheet: 0.31 (1.05), residues: 24 loop : -1.31 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 33 TYR 0.046 0.002 TYR B 88 PHE 0.013 0.001 PHE A 104 TRP 0.012 0.001 TRP K 61 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (14855) covalent geometry : angle 0.67732 / 0.39 (21334) hydrogen bonds : bond 0.04772 / 3.13 ( 844) hydrogen bonds : angle 3.77515 / 2.75 ( 2154) metal coordination : bond 0.00942 / 0.46 ( 8) metal coordination : angle 6.87617 / 2.95 ( 9) link_TRANS : bond 0.00052 / 0.03 ( 2) link_TRANS : angle 0.24762 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 296 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.7477 (m-80) cc_final: 0.7159 (m-10) REVERT: A 60 LEU cc_start: 0.8815 (tp) cc_final: 0.8538 (tp) REVERT: E 73 GLU cc_start: 0.8751 (tt0) cc_final: 0.8484 (tt0) REVERT: E 77 ASP cc_start: 0.8238 (m-30) cc_final: 0.7990 (m-30) REVERT: E 120 MET cc_start: 0.8769 (mmm) cc_final: 0.8238 (mmm) REVERT: F 39 ARG cc_start: 0.9326 (tpp80) cc_final: 0.9006 (mmt-90) REVERT: F 64 ASN cc_start: 0.8640 (m-40) cc_final: 0.8327 (m110) REVERT: F 84 MET cc_start: 0.8126 (tpp) cc_final: 0.7873 (tpp) REVERT: F 92 ARG cc_start: 0.8724 (ttp80) cc_final: 0.8222 (ttp80) REVERT: H 47 GLN cc_start: 0.8823 (tt0) cc_final: 0.8490 (tm-30) REVERT: H 85 LYS cc_start: 0.9359 (mtmm) cc_final: 0.9148 (mtmm) REVERT: H 116 LYS cc_start: 0.9094 (mmtt) cc_final: 0.8661 (mmtp) REVERT: K 68 ARG cc_start: 0.6995 (mpp-170) cc_final: 0.6413 (mpp80) REVERT: L 32 HIS cc_start: 0.8805 (OUTLIER) cc_final: 0.8271 (m-70) REVERT: L 63 LYS cc_start: 0.7552 (tptt) cc_final: 0.7256 (tppt) REVERT: C 56 GLU cc_start: 0.9024 (tp30) cc_final: 0.8645 (tp30) REVERT: C 73 ASN cc_start: 0.9440 (t0) cc_final: 0.9167 (t0) REVERT: C 90 ASP cc_start: 0.8485 (t70) cc_final: 0.8148 (t0) REVERT: G 84 GLN cc_start: 0.9117 (tp-100) cc_final: 0.8480 (tp-100) REVERT: G 92 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7494 (pt0) REVERT: G 104 GLN cc_start: 0.8721 (tt0) cc_final: 0.7769 (tm-30) outliers start: 28 outliers final: 19 residues processed: 308 average time/residue: 0.1366 time to fit residues: 59.0377 Evaluate side-chains 304 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 283 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 60 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.081187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.058685 restraints weight = 62163.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.060192 restraints weight = 31123.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061198 restraints weight = 20940.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.061871 restraints weight = 16741.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.062177 restraints weight = 14645.315| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 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 = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14865 Z= 0.171 Angle : 0.705 11.123 21349 Z= 0.397 Chirality : 0.044 0.250 2418 Planarity : 0.004 0.037 1690 Dihedral : 30.119 161.164 4321 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.96 % Allowed : 24.59 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.27), residues: 987 helix: 1.36 (0.21), residues: 629 sheet: 0.32 (1.07), residues: 24 loop : -1.28 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 33 TYR 0.058 0.002 TYR B 88 PHE 0.013 0.001 PHE K 40 TRP 0.017 0.001 TRP K 61 HIS 0.004 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (14855) covalent geometry : angle 0.69113 / 0.40 (21334) hydrogen bonds : bond 0.04784 / 3.14 ( 844) hydrogen bonds : angle 3.79753 / 2.77 ( 2154) metal coordination : bond 0.01069 / 0.52 ( 8) metal coordination : angle 6.83556 / 2.91 ( 9) link_TRANS : bond 0.00087 / 0.04 ( 2) link_TRANS : angle 0.22407 / 0.08 ( 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 329 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 295 time to evaluate : 0.398 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: 0.8427 (pp20) cc_final: 0.7492 (pp20) REVERT: A 53 ARG cc_start: 0.8553 (tmm-80) cc_final: 0.7965 (tmm-80) REVERT: E 73 GLU cc_start: 0.8760 (tt0) cc_final: 0.8474 (tt0) REVERT: E 77 ASP cc_start: 0.8238 (m-30) cc_final: 0.8007 (m-30) REVERT: E 120 MET cc_start: 0.8795 (mmm) cc_final: 0.8230 (mmm) REVERT: F 39 ARG cc_start: 0.9345 (tpp80) cc_final: 0.9036 (mmt-90) REVERT: F 63 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8385 (mp0) REVERT: F 84 MET cc_start: 0.8190 (tpp) cc_final: 0.7932 (tpp) REVERT: F 92 ARG cc_start: 0.8725 (ttp80) cc_final: 0.8222 (ttp80) REVERT: H 47 GLN cc_start: 0.8835 (tt0) cc_final: 0.8515 (tm-30) REVERT: H 71 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8486 (tm-30) REVERT: H 116 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8656 (mmtp) REVERT: L 32 HIS cc_start: 0.8795 (OUTLIER) cc_final: 0.8253 (m-70) REVERT: L 63 LYS cc_start: 0.7588 (tptt) cc_final: 0.7268 (tppt) REVERT: C 56 GLU cc_start: 0.9055 (tp30) cc_final: 0.8673 (tp30) REVERT: C 73 ASN cc_start: 0.9425 (t0) cc_final: 0.9147 (t0) REVERT: C 90 ASP cc_start: 0.8528 (t70) cc_final: 0.8180 (t0) REVERT: G 84 GLN cc_start: 0.9124 (tp-100) cc_final: 0.8416 (tp-100) outliers start: 34 outliers final: 24 residues processed: 310 average time/residue: 0.1262 time to fit residues: 55.3557 Evaluate side-chains 306 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 280 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 90 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 78 optimal weight: 30.0000 chunk 56 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.081515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.057954 restraints weight = 74720.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.059664 restraints weight = 35635.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.060865 restraints weight = 23327.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.061601 restraints weight = 18120.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.061919 restraints weight = 15685.389| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 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 = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14865 Z= 0.162 Angle : 0.706 11.189 21349 Z= 0.396 Chirality : 0.043 0.256 2418 Planarity : 0.004 0.043 1690 Dihedral : 30.146 161.390 4321 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.85 % Allowed : 25.87 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.27), residues: 987 helix: 1.35 (0.21), residues: 629 sheet: 0.36 (1.07), residues: 24 loop : -1.29 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG K 67 TYR 0.064 0.002 TYR B 88 PHE 0.014 0.001 PHE L 56 TRP 0.015 0.001 TRP K 61 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (14855) covalent geometry : angle 0.69345 / 0.40 (21334) hydrogen bonds : bond 0.04652 / 3.06 ( 844) hydrogen bonds : angle 3.77649 / 2.74 ( 2154) metal coordination : bond 0.00946 / 0.46 ( 8) metal coordination : angle 6.57085 / 2.83 ( 9) link_TRANS : bond 0.00062 / 0.03 ( 2) link_TRANS : angle 0.18102 / 0.06 ( 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 326 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 293 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.8869 (mmm) cc_final: 0.8279 (mmm) REVERT: F 39 ARG cc_start: 0.9355 (tpp80) cc_final: 0.9049 (mmt-90) REVERT: F 67 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7793 (tpm170) REVERT: F 84 MET cc_start: 0.8144 (tpp) cc_final: 0.7656 (tpp) REVERT: F 91 LYS cc_start: 0.8603 (tppt) cc_final: 0.8013 (mmtt) REVERT: F 92 ARG cc_start: 0.8719 (ttp80) cc_final: 0.8212 (ttp80) REVERT: H 47 GLN cc_start: 0.8811 (tt0) cc_final: 0.8487 (tm-30) REVERT: H 71 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8476 (tm-30) REVERT: H 85 LYS cc_start: 0.9385 (mtmm) cc_final: 0.9174 (mtmm) REVERT: H 116 LYS cc_start: 0.9088 (mmtt) cc_final: 0.8651 (mmtp) REVERT: L 32 HIS cc_start: 0.8785 (OUTLIER) cc_final: 0.8250 (m-70) REVERT: L 63 LYS cc_start: 0.7595 (tptt) cc_final: 0.7277 (tppt) REVERT: C 56 GLU cc_start: 0.9026 (tp30) cc_final: 0.8628 (tp30) REVERT: C 73 ASN cc_start: 0.9381 (t0) cc_final: 0.9090 (t0) REVERT: C 90 ASP cc_start: 0.8517 (t70) cc_final: 0.8168 (t0) REVERT: G 57 TYR cc_start: 0.8714 (t80) cc_final: 0.8466 (t80) REVERT: G 84 GLN cc_start: 0.9129 (tp-100) cc_final: 0.8388 (tp-100) outliers start: 33 outliers final: 21 residues processed: 307 average time/residue: 0.1214 time to fit residues: 51.9019 Evaluate side-chains 302 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 279 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 66 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 96 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 58 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.079810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.055102 restraints weight = 107980.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.057056 restraints weight = 44664.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.058313 restraints weight = 27338.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.059109 restraints weight = 20668.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.059473 restraints weight = 17588.035| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 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 = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2244 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= 0.218 Angle : 0.753 11.651 21349 Z= 0.416 Chirality : 0.045 0.272 2418 Planarity : 0.005 0.048 1690 Dihedral : 30.301 161.681 4321 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.50 % Allowed : 26.46 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.27), residues: 987 helix: 1.23 (0.20), residues: 629 sheet: 0.42 (1.08), residues: 24 loop : -1.30 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 67 TYR 0.059 0.003 TYR B 88 PHE 0.016 0.002 PHE A 104 TRP 0.015 0.001 TRP K 61 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.22 (14855) covalent geometry : angle 0.74081 / 0.42 (21334) hydrogen bonds : bond 0.05424 / 3.63 ( 844) hydrogen bonds : angle 3.89776 / 2.83 ( 2154) metal coordination : bond 0.01939 / 0.98 ( 8) metal coordination : angle 6.66146 / 2.89 ( 9) link_TRANS : bond 0.00190 / 0.09 ( 2) link_TRANS : angle 0.34689 / 0.13 ( 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 315 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 285 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8616 (tmm-80) cc_final: 0.8108 (tmm-80) REVERT: E 77 ASP cc_start: 0.8209 (m-30) cc_final: 0.7970 (m-30) REVERT: E 120 MET cc_start: 0.8932 (mmm) cc_final: 0.8278 (mmm) REVERT: F 39 ARG cc_start: 0.9367 (tpp80) cc_final: 0.9123 (mmt-90) REVERT: F 84 MET cc_start: 0.8219 (tpp) cc_final: 0.7964 (tpp) REVERT: F 92 ARG cc_start: 0.8795 (ttp80) cc_final: 0.8320 (ttp80) REVERT: H 47 GLN cc_start: 0.8852 (tt0) cc_final: 0.8522 (tm-30) REVERT: H 116 LYS cc_start: 0.9130 (mmtt) cc_final: 0.8747 (mmtp) REVERT: L 63 LYS cc_start: 0.7626 (tptt) cc_final: 0.7307 (tppt) REVERT: C 56 GLU cc_start: 0.9047 (tp30) cc_final: 0.8630 (tp30) REVERT: C 73 ASN cc_start: 0.9382 (t0) cc_final: 0.9092 (t0) REVERT: C 90 ASP cc_start: 0.8542 (t70) cc_final: 0.8215 (t0) outliers start: 30 outliers final: 24 residues processed: 298 average time/residue: 0.1275 time to fit residues: 52.7929 Evaluate side-chains 298 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 274 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain 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 66 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 9 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.080444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.056282 restraints weight = 86521.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.058111 restraints weight = 38754.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.059315 restraints weight = 24591.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.060081 restraints weight = 18842.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.060415 restraints weight = 16174.020| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 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 = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14865 Z= 0.183 Angle : 0.741 11.891 21349 Z= 0.410 Chirality : 0.044 0.270 2418 Planarity : 0.004 0.049 1690 Dihedral : 30.315 161.088 4321 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.85 % Allowed : 25.76 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.27), residues: 987 helix: 1.20 (0.20), residues: 629 sheet: 0.38 (1.11), residues: 24 loop : -1.30 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 67 TYR 0.038 0.002 TYR B 88 PHE 0.015 0.001 PHE A 104 TRP 0.020 0.002 TRP K 61 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (14855) covalent geometry : angle 0.72893 / 0.41 (21334) hydrogen bonds : bond 0.04938 / 3.28 ( 844) hydrogen bonds : angle 3.82809 / 2.78 ( 2154) metal coordination : bond 0.01491 / 0.74 ( 8) metal coordination : angle 6.54066 / 2.78 ( 9) link_TRANS : bond 0.00086 / 0.04 ( 2) link_TRANS : angle 0.27417 / 0.10 ( 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 315 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 282 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8621 (tmm-80) cc_final: 0.8110 (tmm-80) REVERT: E 77 ASP cc_start: 0.8203 (m-30) cc_final: 0.7955 (m-30) REVERT: E 120 MET cc_start: 0.8938 (mmm) cc_final: 0.8268 (mmm) REVERT: F 39 ARG cc_start: 0.9359 (tpp80) cc_final: 0.9120 (mmt-90) REVERT: F 92 ARG cc_start: 0.8783 (ttp80) cc_final: 0.8163 (ttp80) REVERT: H 47 GLN cc_start: 0.8822 (tt0) cc_final: 0.8507 (tm-30) REVERT: H 85 LYS cc_start: 0.9384 (mtmm) cc_final: 0.9169 (mtmm) REVERT: L 63 LYS cc_start: 0.7540 (tptt) cc_final: 0.7205 (tppt) REVERT: C 56 GLU cc_start: 0.9049 (tp30) cc_final: 0.8639 (tp30) REVERT: C 63 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9174 (mm) REVERT: C 73 ASN cc_start: 0.9349 (t0) cc_final: 0.9052 (t0) REVERT: C 90 ASP cc_start: 0.8564 (t70) cc_final: 0.8188 (t0) outliers start: 33 outliers final: 28 residues processed: 297 average time/residue: 0.1242 time to fit residues: 51.3187 Evaluate side-chains 304 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 275 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 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 66 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 67 ARG Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 92 GLU 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: 3.9990 chunk 77 optimal weight: 20.0000 chunk 35 optimal weight: 0.0970 chunk 83 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 51 optimal weight: 0.9990 chunk 86 optimal weight: 0.0010 chunk 102 optimal weight: 0.3980 chunk 74 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.082431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.058025 restraints weight = 105944.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.060071 restraints weight = 43248.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.061357 restraints weight = 26218.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.062217 restraints weight = 19668.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.062598 restraints weight = 16602.739| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 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 = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14865 Z= 0.159 Angle : 0.748 11.794 21349 Z= 0.413 Chirality : 0.044 0.261 2418 Planarity : 0.004 0.037 1690 Dihedral : 30.219 162.050 4321 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.03 % Allowed : 27.74 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.27), residues: 987 helix: 1.20 (0.20), residues: 628 sheet: 0.45 (1.10), residues: 24 loop : -1.24 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 67 TYR 0.045 0.002 TYR B 88 PHE 0.013 0.001 PHE A 104 TRP 0.025 0.003 TRP K 77 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (14855) covalent geometry : angle 0.73707 / 0.41 (21334) hydrogen bonds : bond 0.04580 / 3.03 ( 844) hydrogen bonds : angle 3.75507 / 2.74 ( 2154) metal coordination : bond 0.00607 / 0.30 ( 8) metal coordination : angle 6.23667 / 2.56 ( 9) link_TRANS : bond 0.00037 / 0.02 ( 2) link_TRANS : angle 0.16651 / 0.07 ( 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 325 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 299 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8653 (tmm-80) cc_final: 0.8129 (tmm-80) REVERT: A 125 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8834 (mm-40) REVERT: B 54 THR cc_start: 0.9352 (m) cc_final: 0.9104 (p) REVERT: E 77 ASP cc_start: 0.8123 (m-30) cc_final: 0.7892 (m-30) REVERT: E 120 MET cc_start: 0.8923 (mmm) cc_final: 0.8286 (mmm) REVERT: F 39 ARG cc_start: 0.9350 (tpp80) cc_final: 0.9099 (mmt-90) REVERT: F 63 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8555 (pm20) REVERT: F 92 ARG cc_start: 0.8811 (ttp80) cc_final: 0.8419 (ttp80) REVERT: H 47 GLN cc_start: 0.8802 (tt0) cc_final: 0.8496 (tm-30) REVERT: H 85 LYS cc_start: 0.9402 (mtmm) cc_final: 0.9161 (mtmm) REVERT: L 32 HIS cc_start: 0.8705 (OUTLIER) cc_final: 0.8163 (m-70) REVERT: L 63 LYS cc_start: 0.7592 (tptt) cc_final: 0.7257 (tppt) REVERT: C 63 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9169 (mm) REVERT: C 73 ASN cc_start: 0.9290 (t0) cc_final: 0.9026 (t0) REVERT: C 90 ASP cc_start: 0.8476 (t70) cc_final: 0.8127 (t0) REVERT: G 57 TYR cc_start: 0.8647 (t80) cc_final: 0.8416 (t80) outliers start: 26 outliers final: 17 residues processed: 309 average time/residue: 0.1236 time to fit residues: 53.5166 Evaluate side-chains 296 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 276 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 86 LEU 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 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: 0.8980 chunk 119 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 60 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.0170 chunk 40 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 53 optimal weight: 30.0000 chunk 2 optimal weight: 3.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS E 68 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.082247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.057795 restraints weight = 93157.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.059718 restraints weight = 40378.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.060982 restraints weight = 25239.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.061597 restraints weight = 19214.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.062165 restraints weight = 16784.642| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14865 Z= 0.162 Angle : 0.766 12.173 21349 Z= 0.419 Chirality : 0.044 0.291 2418 Planarity : 0.004 0.038 1690 Dihedral : 30.228 163.282 4321 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.15 % Allowed : 28.90 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.27), residues: 987 helix: 1.14 (0.21), residues: 627 sheet: 0.44 (1.09), residues: 24 loop : -1.24 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 67 TYR 0.081 0.003 TYR D 83 PHE 0.016 0.002 PHE H 70 TRP 0.025 0.003 TRP K 61 HIS 0.010 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (14855) covalent geometry : angle 0.75511 / 0.42 (21334) hydrogen bonds : bond 0.04594 / 3.05 ( 844) hydrogen bonds : angle 3.80259 / 2.77 ( 2154) metal coordination : bond 0.00686 / 0.34 ( 8) metal coordination : angle 6.27562 / 2.60 ( 9) link_TRANS : bond 0.00016 / 0.01 ( 2) link_TRANS : angle 0.11925 / 0.04 ( 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 308 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 281 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8668 (tmm-80) cc_final: 0.8119 (tmm-80) REVERT: A 64 LYS cc_start: 0.9086 (tppp) cc_final: 0.8836 (tppp) REVERT: B 54 THR cc_start: 0.9359 (m) cc_final: 0.9125 (p) REVERT: D 109 HIS cc_start: 0.8210 (m-70) cc_final: 0.6891 (m170) REVERT: E 64 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8266 (mtpt) REVERT: E 120 MET cc_start: 0.8932 (mmm) cc_final: 0.8320 (mmm) REVERT: F 39 ARG cc_start: 0.9360 (tpp80) cc_final: 0.9098 (mmt-90) REVERT: F 92 ARG cc_start: 0.8854 (ttp80) cc_final: 0.8304 (ttp80) REVERT: H 47 GLN cc_start: 0.8785 (tt0) cc_final: 0.8483 (tm-30) REVERT: H 85 LYS cc_start: 0.9405 (mtmm) cc_final: 0.9177 (mtmm) REVERT: K 65 HIS cc_start: 0.8648 (m90) cc_final: 0.8350 (m90) REVERT: L 32 HIS cc_start: 0.8729 (OUTLIER) cc_final: 0.8223 (m-70) REVERT: L 63 LYS cc_start: 0.7559 (tptt) cc_final: 0.7229 (tppt) REVERT: C 63 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9135 (mm) REVERT: C 73 ASN cc_start: 0.9283 (t0) cc_final: 0.9005 (t0) REVERT: C 90 ASP cc_start: 0.8483 (t70) cc_final: 0.8075 (t0) REVERT: G 57 TYR cc_start: 0.8666 (t80) cc_final: 0.8439 (t80) REVERT: G 64 GLU cc_start: 0.8616 (tp30) cc_final: 0.8399 (tp30) outliers start: 27 outliers final: 18 residues processed: 292 average time/residue: 0.1368 time to fit residues: 55.8866 Evaluate side-chains 292 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 271 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR 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 E residue 60 LEU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 67 optimal weight: 30.0000 chunk 66 optimal weight: 50.0000 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.079210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.055309 restraints weight = 68508.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.056889 restraints weight = 34827.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.057938 restraints weight = 23792.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.058555 restraints weight = 19066.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.058847 restraints weight = 16843.531| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 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 = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14865 Z= 0.254 Angle : 0.831 12.029 21349 Z= 0.449 Chirality : 0.047 0.296 2418 Planarity : 0.006 0.058 1690 Dihedral : 30.497 162.958 4321 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.68 % Allowed : 29.02 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.26), residues: 987 helix: 0.97 (0.20), residues: 630 sheet: 0.01 (0.97), residues: 29 loop : -1.27 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG G 99 TYR 0.095 0.004 TYR B 88 PHE 0.019 0.002 PHE A 104 TRP 0.056 0.005 TRP L 33 HIS 0.009 0.002 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.25 (14855) covalent geometry : angle 0.82001 / 0.45 (21334) hydrogen bonds : bond 0.06193 / 4.21 ( 844) hydrogen bonds : angle 4.11439 / 2.97 ( 2154) metal coordination : bond 0.02331 / 1.16 ( 8) metal coordination : angle 6.65279 / 3.01 ( 9) link_TRANS : bond 0.00225 / 0.11 ( 2) link_TRANS : angle 0.38088 / 0.14 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2706.45 seconds wall clock time: 47 minutes 20.45 seconds (2840.45 seconds total)