Starting phenix.real_space_refine on Mon Jun 16 08:44:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u14_41801/06_2025/8u14_41801.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u14_41801/06_2025/8u14_41801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u14_41801/06_2025/8u14_41801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u14_41801/06_2025/8u14_41801.map" model { file = "/net/cci-nas-00/data/ceres_data/8u14_41801/06_2025/8u14_41801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u14_41801/06_2025/8u14_41801.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.51, per 1000 atoms: 0.61 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: 3.34 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 5.86 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: 4.71 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3398 1.34 - 1.46: 4244 1.46 - 1.58: 6583 1.58 - 1.70: 584 1.70 - 1.82: 46 Bond restraints: 14855 Sorted by residual: bond pdb=" C HIS H 49 " pdb=" O HIS H 49 " ideal model delta sigma weight residual 1.249 1.237 0.012 8.50e-03 1.38e+04 1.91e+00 bond pdb=" CB LYS B 59 " pdb=" CG LYS B 59 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.40e+00 bond pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 1.460 1.476 -0.017 1.42e-02 4.96e+03 1.35e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.32e+00 ... (remaining 14850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 20629 1.65 - 3.29: 625 3.29 - 4.94: 58 4.94 - 6.59: 16 6.59 - 8.23: 6 Bond angle restraints: 21334 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 113.53 108.56 4.97 9.80e-01 1.04e+00 2.57e+01 angle pdb=" N GLU F 63 " pdb=" CA GLU F 63 " pdb=" CB GLU F 63 " ideal model delta sigma weight residual 110.39 116.07 -5.68 1.66e+00 3.63e-01 1.17e+01 angle pdb=" CA GLU F 63 " pdb=" CB GLU F 63 " pdb=" CG GLU F 63 " ideal model delta sigma weight residual 114.10 120.81 -6.71 2.00e+00 2.50e-01 1.13e+01 angle pdb=" CB LYS B 59 " pdb=" CG LYS B 59 " pdb=" CD LYS B 59 " ideal model delta sigma weight residual 111.30 118.47 -7.17 2.30e+00 1.89e-01 9.73e+00 angle pdb=" N ARG B 36 " pdb=" CA ARG B 36 " pdb=" CB ARG B 36 " ideal model delta sigma weight residual 110.28 114.90 -4.62 1.55e+00 4.16e-01 8.88e+00 ... (remaining 21329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.61: 6645 31.61 - 63.22: 1529 63.22 - 94.84: 42 94.84 - 126.45: 0 126.45 - 158.06: 2 Dihedral angle restraints: 8218 sinusoidal: 5288 harmonic: 2930 Sorted by residual: dihedral pdb=" CA ASN B 25 " pdb=" C ASN B 25 " pdb=" N ILE B 26 " pdb=" CA ILE B 26 " ideal model delta harmonic sigma weight residual 180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 61.94 158.06 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 65.92 154.08 1 3.50e+01 8.16e-04 1.49e+01 ... (remaining 8215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1787 0.034 - 0.069: 477 0.069 - 0.103: 120 0.103 - 0.138: 29 0.138 - 0.172: 5 Chirality restraints: 2418 Sorted by residual: chirality pdb=" CA GLU F 63 " pdb=" N GLU F 63 " pdb=" C GLU F 63 " pdb=" CB GLU F 63 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA GLN E 125 " pdb=" N GLN E 125 " pdb=" C GLN E 125 " pdb=" CB GLN E 125 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 2415 not shown) Planarity restraints: 1692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.024 2.00e-02 2.50e+03 1.04e-02 2.98e+00 pdb=" N9 DA I -35 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C LYS F 59 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS F 59 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL F 60 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 73 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" CD GLU A 73 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU A 73 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A 73 " -0.010 2.00e-02 2.50e+03 ... (remaining 1689 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 466 2.68 - 3.23: 13143 3.23 - 3.79: 27192 3.79 - 4.34: 32816 4.34 - 4.90: 46740 Nonbonded interactions: 120357 Sorted by model distance: nonbonded pdb=" O ARG K 63 " pdb=" NH1 ARG K 67 " model vdw 2.124 3.120 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.150 2.496 nonbonded pdb=" OE1 GLN D 95 " pdb=" OH TYR C 50 " model vdw 2.160 3.040 nonbonded pdb=" NE2 HIS B 75 " pdb=" OE1 GLU D 93 " model vdw 2.204 3.120 nonbonded pdb=" OE2 GLU H 105 " pdb=" NH1 ARG K 67 " model vdw 2.223 3.120 ... (remaining 120352 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 119) } ncs_group { reference = (chain 'D' and resid 31 through 123) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 38.700 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14865 Z= 0.159 Angle : 0.665 12.911 21349 Z= 0.372 Chirality : 0.035 0.172 2418 Planarity : 0.004 0.041 1690 Dihedral : 26.360 158.059 6320 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP K 61 HIS 0.003 0.001 HIS G 31 PHE 0.017 0.001 PHE E 78 TYR 0.024 0.001 TYR F 88 ARG 0.016 0.001 ARG B 36 Details of bonding type rmsd link_TRANS : bond 0.00188 ( 2) link_TRANS : angle 0.84845 ( 6) hydrogen bonds : bond 0.10380 ( 844) hydrogen bonds : angle 4.37418 ( 2154) metal coordination : bond 0.00526 ( 8) metal coordination : angle 7.88243 ( 9) covalent geometry : bond 0.00335 (14855) covalent geometry : angle 0.64522 (21334) *********************** 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 : 1.021 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: 0.3233 time to fit residues: 154.7879 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 : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 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 ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.081680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.058289 restraints weight = 76087.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.060070 restraints weight = 35899.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061257 restraints weight = 23504.912| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14865 Z= 0.196 Angle : 0.677 14.110 21349 Z= 0.374 Chirality : 0.038 0.177 2418 Planarity : 0.005 0.035 1690 Dihedral : 29.614 156.743 4321 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.10 % Allowed : 18.07 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 987 helix: 1.32 (0.20), residues: 631 sheet: 0.31 (0.98), residues: 24 loop : -1.23 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP L 33 HIS 0.006 0.001 HIS K 65 PHE 0.018 0.002 PHE A 104 TYR 0.027 0.002 TYR B 88 ARG 0.006 0.001 ARG L 136 Details of bonding type rmsd link_TRANS : bond 0.00062 ( 2) link_TRANS : angle 0.18495 ( 6) hydrogen bonds : bond 0.04685 ( 844) hydrogen bonds : angle 3.84715 ( 2154) metal coordination : bond 0.01162 ( 8) metal coordination : angle 8.25545 ( 9) covalent geometry : bond 0.00432 (14855) covalent geometry : angle 0.65611 (21334) *********************** 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 321 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 303 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8994 (tppp) cc_final: 0.8777 (tppp) REVERT: A 125 GLN cc_start: 0.8449 (mp10) cc_final: 0.8093 (mp10) REVERT: B 84 MET cc_start: 0.9290 (tpp) cc_final: 0.8731 (tpp) REVERT: D 33 ARG cc_start: 0.8683 (ttm-80) cc_final: 0.8104 (tpp80) REVERT: D 79 ARG cc_start: 0.8646 (ttm110) cc_final: 0.8421 (ttm110) REVERT: D 95 GLN cc_start: 0.9046 (tp40) cc_final: 0.8537 (tp40) REVERT: E 77 ASP cc_start: 0.8267 (m-30) cc_final: 0.8001 (m-30) REVERT: E 120 MET cc_start: 0.8785 (mmm) cc_final: 0.8366 (mmm) REVERT: F 84 MET cc_start: 0.8131 (tpp) cc_final: 0.7823 (tpp) REVERT: F 92 ARG cc_start: 0.8812 (ttp80) cc_final: 0.8277 (ttp80) REVERT: H 47 GLN cc_start: 0.8840 (tt0) cc_final: 0.8493 (tm-30) REVERT: H 71 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8449 (tm-30) REVERT: K 86 ARG cc_start: 0.9400 (pmt170) cc_final: 0.9054 (pmt170) REVERT: L 63 LYS cc_start: 0.7662 (tptt) cc_final: 0.7365 (tppt) REVERT: C 73 ASN cc_start: 0.9497 (t0) cc_final: 0.9246 (t0) REVERT: C 90 ASP cc_start: 0.8557 (t70) cc_final: 0.8203 (t0) REVERT: G 104 GLN cc_start: 0.8683 (tt0) cc_final: 0.7871 (tm-30) outliers start: 18 outliers final: 9 residues processed: 310 average time/residue: 0.3046 time to fit residues: 128.8613 Evaluate side-chains 294 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 285 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 6 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 0.1980 chunk 102 optimal weight: 0.7980 chunk 121 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN G 38 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 = 0.082561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.059161 restraints weight = 69158.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.060904 restraints weight = 34140.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.062024 restraints weight = 22847.141| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1693 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= 0.161 Angle : 0.652 12.071 21349 Z= 0.361 Chirality : 0.037 0.174 2418 Planarity : 0.004 0.037 1690 Dihedral : 29.615 156.391 4321 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.68 % Allowed : 20.63 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 987 helix: 1.44 (0.20), residues: 629 sheet: 0.39 (1.02), residues: 24 loop : -1.28 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 61 HIS 0.003 0.001 HIS G 31 PHE 0.012 0.001 PHE A 104 TYR 0.032 0.002 TYR B 88 ARG 0.005 0.001 ARG K 67 Details of bonding type rmsd link_TRANS : bond 0.00024 ( 2) link_TRANS : angle 0.19676 ( 6) hydrogen bonds : bond 0.04146 ( 844) hydrogen bonds : angle 3.67842 ( 2154) metal coordination : bond 0.00628 ( 8) metal coordination : angle 7.23041 ( 9) covalent geometry : bond 0.00349 (14855) covalent geometry : angle 0.63470 (21334) *********************** 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 331 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 308 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8821 (tppp) cc_final: 0.8505 (tppp) REVERT: A 106 ASP cc_start: 0.8789 (m-30) cc_final: 0.8499 (m-30) REVERT: A 125 GLN cc_start: 0.8364 (mt0) cc_final: 0.8078 (mp10) REVERT: B 54 THR cc_start: 0.9449 (m) cc_final: 0.9192 (p) REVERT: D 33 ARG cc_start: 0.8698 (ttm-80) cc_final: 0.8178 (tpp80) REVERT: D 79 ARG cc_start: 0.8673 (ttm110) cc_final: 0.8291 (ttm110) REVERT: D 95 GLN cc_start: 0.9030 (tp40) cc_final: 0.8573 (tp40) REVERT: E 73 GLU cc_start: 0.8782 (tt0) cc_final: 0.8464 (tt0) REVERT: E 77 ASP cc_start: 0.8260 (m-30) cc_final: 0.8023 (m-30) REVERT: E 90 MET cc_start: 0.8105 (mmt) cc_final: 0.7750 (mmp) REVERT: E 120 MET cc_start: 0.8934 (mmm) cc_final: 0.8443 (mmm) REVERT: F 39 ARG cc_start: 0.9317 (tpp80) cc_final: 0.8680 (mmm-85) REVERT: F 84 MET cc_start: 0.8050 (tpp) cc_final: 0.7754 (tpp) REVERT: F 92 ARG cc_start: 0.8719 (ttp80) cc_final: 0.8285 (ttp80) REVERT: H 47 GLN cc_start: 0.8787 (tt0) cc_final: 0.8479 (tm-30) REVERT: H 71 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8512 (tm-30) REVERT: H 85 LYS cc_start: 0.9356 (mtmm) cc_final: 0.9150 (mtmm) REVERT: H 93 GLU cc_start: 0.8880 (mp0) cc_final: 0.8660 (mp0) REVERT: H 116 LYS cc_start: 0.9054 (mmtt) cc_final: 0.8732 (mmtp) REVERT: L 63 LYS cc_start: 0.7579 (tptt) cc_final: 0.7236 (tppt) REVERT: C 73 ASN cc_start: 0.9431 (t0) cc_final: 0.9158 (t0) REVERT: C 90 ASP cc_start: 0.8557 (t70) cc_final: 0.8210 (t0) REVERT: G 57 TYR cc_start: 0.8698 (t80) cc_final: 0.8487 (t80) REVERT: G 84 GLN cc_start: 0.9128 (tp-100) cc_final: 0.8552 (tp-100) REVERT: G 90 ASP cc_start: 0.8596 (t70) cc_final: 0.8139 (t0) REVERT: G 104 GLN cc_start: 0.8674 (tt0) cc_final: 0.7809 (tm-30) outliers start: 23 outliers final: 17 residues processed: 318 average time/residue: 0.3031 time to fit residues: 133.5114 Evaluate side-chains 303 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 286 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 119 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 92 optimal weight: 30.0000 chunk 60 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.080336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.055882 restraints weight = 92386.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.057724 restraints weight = 40858.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.058959 restraints weight = 25884.793| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 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 = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14865 Z= 0.218 Angle : 0.671 12.301 21349 Z= 0.372 Chirality : 0.038 0.158 2418 Planarity : 0.004 0.035 1690 Dihedral : 29.816 154.810 4321 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.96 % Allowed : 22.96 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.27), residues: 987 helix: 1.47 (0.21), residues: 630 sheet: 0.43 (1.07), residues: 24 loop : -1.21 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 61 HIS 0.004 0.001 HIS C 31 PHE 0.009 0.001 PHE H 70 TYR 0.042 0.002 TYR B 88 ARG 0.005 0.001 ARG C 35 Details of bonding type rmsd link_TRANS : bond 0.00135 ( 2) link_TRANS : angle 0.27679 ( 6) hydrogen bonds : bond 0.04943 ( 844) hydrogen bonds : angle 3.74375 ( 2154) metal coordination : bond 0.01832 ( 8) metal coordination : angle 7.82513 ( 9) covalent geometry : bond 0.00487 (14855) covalent geometry : angle 0.65221 (21334) *********************** 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 327 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 293 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 ARG cc_start: 0.8751 (ttm-80) cc_final: 0.8244 (tpp80) REVERT: E 73 GLU cc_start: 0.8700 (tt0) cc_final: 0.8434 (tt0) REVERT: E 77 ASP cc_start: 0.8243 (m-30) cc_final: 0.8024 (m-30) REVERT: E 90 MET cc_start: 0.8211 (mmt) cc_final: 0.7875 (mmp) REVERT: E 120 MET cc_start: 0.8965 (mmm) cc_final: 0.8437 (mmm) REVERT: F 84 MET cc_start: 0.8199 (tpp) cc_final: 0.7937 (tpp) REVERT: F 92 ARG cc_start: 0.8745 (ttp80) cc_final: 0.8386 (ttp80) REVERT: H 47 GLN cc_start: 0.8805 (tt0) cc_final: 0.8497 (tm-30) REVERT: H 71 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8535 (tm-30) REVERT: H 85 LYS cc_start: 0.9357 (mtmm) cc_final: 0.9122 (mtmm) REVERT: H 116 LYS cc_start: 0.9089 (mmtt) cc_final: 0.8702 (mmtp) REVERT: K 46 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8638 (mmtm) REVERT: K 64 TYR cc_start: 0.8454 (t80) cc_final: 0.8188 (t80) REVERT: L 63 LYS cc_start: 0.7548 (tptt) cc_final: 0.7215 (tppt) REVERT: C 73 ASN cc_start: 0.9396 (t0) cc_final: 0.9107 (t0) REVERT: C 90 ASP cc_start: 0.8590 (t70) cc_final: 0.8219 (t0) REVERT: G 90 ASP cc_start: 0.8615 (t70) cc_final: 0.8403 (t0) REVERT: G 104 GLN cc_start: 0.8725 (tt0) cc_final: 0.7776 (tm-30) outliers start: 34 outliers final: 27 residues processed: 307 average time/residue: 0.3068 time to fit residues: 128.9640 Evaluate side-chains 305 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 278 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 125 GLN 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 H residue 98 VAL Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 44 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 0.0970 chunk 55 optimal weight: 7.9990 chunk 105 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN G 38 ASN G 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.082554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.059101 restraints weight = 62397.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.060638 restraints weight = 32302.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.061668 restraints weight = 22217.537| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14865 Z= 0.156 Angle : 0.657 12.397 21349 Z= 0.362 Chirality : 0.037 0.182 2418 Planarity : 0.004 0.038 1690 Dihedral : 29.726 154.821 4321 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.61 % Allowed : 24.83 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.27), residues: 987 helix: 1.47 (0.21), residues: 628 sheet: 0.44 (1.07), residues: 24 loop : -1.17 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 61 HIS 0.003 0.001 HIS G 31 PHE 0.012 0.001 PHE E 67 TYR 0.051 0.002 TYR B 88 ARG 0.007 0.001 ARG F 39 Details of bonding type rmsd link_TRANS : bond 0.00022 ( 2) link_TRANS : angle 0.13651 ( 6) hydrogen bonds : bond 0.04002 ( 844) hydrogen bonds : angle 3.62026 ( 2154) metal coordination : bond 0.00610 ( 8) metal coordination : angle 7.11768 ( 9) covalent geometry : bond 0.00341 (14855) covalent geometry : angle 0.64076 (21334) *********************** 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 327 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 296 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8466 (pp20) cc_final: 0.7731 (pp20) REVERT: A 53 ARG cc_start: 0.8663 (tmm-80) cc_final: 0.8118 (tmm-80) REVERT: A 76 GLN cc_start: 0.8883 (pp30) cc_final: 0.8681 (pp30) REVERT: D 79 ARG cc_start: 0.8675 (ttm110) cc_final: 0.8335 (ttm110) REVERT: E 73 GLU cc_start: 0.8728 (tt0) cc_final: 0.8410 (tt0) REVERT: E 77 ASP cc_start: 0.8180 (m-30) cc_final: 0.7959 (m-30) REVERT: E 90 MET cc_start: 0.8160 (mmt) cc_final: 0.7851 (mmp) REVERT: E 120 MET cc_start: 0.8971 (mmm) cc_final: 0.8418 (mmm) REVERT: F 63 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8408 (mp0) REVERT: F 84 MET cc_start: 0.8112 (tpp) cc_final: 0.7875 (tpp) REVERT: F 92 ARG cc_start: 0.8726 (ttp80) cc_final: 0.8346 (ttp80) REVERT: H 47 GLN cc_start: 0.8798 (tt0) cc_final: 0.8502 (tm-30) REVERT: H 71 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8571 (tm-30) REVERT: H 93 GLU cc_start: 0.8958 (mp0) cc_final: 0.8673 (mp0) REVERT: H 116 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8680 (mmtp) REVERT: L 32 HIS cc_start: 0.8620 (OUTLIER) cc_final: 0.8136 (m-70) REVERT: C 73 ASN cc_start: 0.9333 (t0) cc_final: 0.9024 (t0) REVERT: C 90 ASP cc_start: 0.8530 (t70) cc_final: 0.8174 (t0) REVERT: G 57 TYR cc_start: 0.8687 (t80) cc_final: 0.8478 (t80) REVERT: G 64 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7388 (tp30) REVERT: G 84 GLN cc_start: 0.9112 (tp-100) cc_final: 0.8728 (tp-100) outliers start: 31 outliers final: 22 residues processed: 306 average time/residue: 0.3271 time to fit residues: 137.1209 Evaluate side-chains 308 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 283 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 E residue 60 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 63 GLU 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 72 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 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 64 GLU 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 70 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 92 optimal weight: 30.0000 chunk 86 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.079259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.054994 restraints weight = 88164.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.056761 restraints weight = 39746.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.057923 restraints weight = 25374.730| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14865 Z= 0.259 Angle : 0.713 12.898 21349 Z= 0.391 Chirality : 0.040 0.199 2418 Planarity : 0.005 0.051 1690 Dihedral : 29.991 153.344 4321 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.78 % Allowed : 25.29 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.26), residues: 987 helix: 1.37 (0.20), residues: 626 sheet: 0.08 (0.93), residues: 29 loop : -1.20 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 61 HIS 0.008 0.001 HIS L 75 PHE 0.015 0.002 PHE H 70 TYR 0.053 0.002 TYR B 88 ARG 0.015 0.001 ARG K 67 Details of bonding type rmsd link_TRANS : bond 0.00158 ( 2) link_TRANS : angle 0.34011 ( 6) hydrogen bonds : bond 0.05376 ( 844) hydrogen bonds : angle 3.83925 ( 2154) metal coordination : bond 0.02412 ( 8) metal coordination : angle 7.42308 ( 9) covalent geometry : bond 0.00582 (14855) covalent geometry : angle 0.69632 (21334) *********************** 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 329 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 288 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8990 (pp30) cc_final: 0.8787 (pp30) REVERT: B 59 LYS cc_start: 0.9166 (tppt) cc_final: 0.8410 (tptp) REVERT: B 88 TYR cc_start: 0.8892 (m-80) cc_final: 0.8483 (m-80) REVERT: D 83 TYR cc_start: 0.7893 (m-10) cc_final: 0.7378 (m-10) REVERT: E 73 GLU cc_start: 0.8725 (tt0) cc_final: 0.8423 (tt0) REVERT: E 77 ASP cc_start: 0.8182 (m-30) cc_final: 0.7945 (m-30) REVERT: E 90 MET cc_start: 0.8172 (mmt) cc_final: 0.7854 (mmp) REVERT: E 120 MET cc_start: 0.8981 (mmm) cc_final: 0.8298 (mmm) REVERT: F 63 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8444 (mp0) REVERT: F 67 ARG cc_start: 0.8292 (tpm170) cc_final: 0.7897 (ttm-80) REVERT: F 84 MET cc_start: 0.8271 (tpp) cc_final: 0.8019 (tpp) REVERT: F 92 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8257 (ttp80) REVERT: H 47 GLN cc_start: 0.8846 (tt0) cc_final: 0.8538 (tm-30) REVERT: H 71 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8549 (tm-30) REVERT: H 93 GLU cc_start: 0.8942 (mp0) cc_final: 0.8669 (mp0) REVERT: H 116 LYS cc_start: 0.9096 (mmtt) cc_final: 0.8707 (mmtp) REVERT: K 46 LYS cc_start: 0.8557 (mmtm) cc_final: 0.8344 (mmtt) REVERT: K 64 TYR cc_start: 0.8478 (t80) cc_final: 0.8275 (t80) REVERT: C 73 ASN cc_start: 0.9395 (t0) cc_final: 0.9090 (t0) REVERT: C 90 ASP cc_start: 0.8594 (t70) cc_final: 0.8264 (t0) REVERT: G 64 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7644 (tp30) REVERT: G 68 ASN cc_start: 0.9080 (m-40) cc_final: 0.8840 (m110) outliers start: 41 outliers final: 32 residues processed: 306 average time/residue: 0.3286 time to fit residues: 139.3213 Evaluate side-chains 312 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 278 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 82 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 H residue 98 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU 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 101 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.081738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.057784 restraints weight = 76261.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.059512 restraints weight = 36158.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.060668 restraints weight = 23577.385| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 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 = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14865 Z= 0.165 Angle : 0.688 13.139 21349 Z= 0.377 Chirality : 0.038 0.204 2418 Planarity : 0.004 0.041 1690 Dihedral : 29.897 153.235 4321 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.96 % Allowed : 27.04 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 987 helix: 1.40 (0.20), residues: 626 sheet: 0.32 (0.94), residues: 29 loop : -1.15 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 61 HIS 0.004 0.001 HIS L 75 PHE 0.014 0.001 PHE H 70 TYR 0.044 0.002 TYR B 88 ARG 0.010 0.001 ARG K 67 Details of bonding type rmsd link_TRANS : bond 0.00028 ( 2) link_TRANS : angle 0.20839 ( 6) hydrogen bonds : bond 0.04065 ( 844) hydrogen bonds : angle 3.67228 ( 2154) metal coordination : bond 0.01007 ( 8) metal coordination : angle 6.97934 ( 9) covalent geometry : bond 0.00364 (14855) covalent geometry : angle 0.67351 (21334) *********************** 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 326 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 292 time to evaluate : 1.145 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: 0.8725 (tmm-80) cc_final: 0.8163 (tmm-80) REVERT: A 76 GLN cc_start: 0.8930 (pp30) cc_final: 0.8691 (pp30) REVERT: E 90 MET cc_start: 0.8093 (mmt) cc_final: 0.7788 (mmp) REVERT: E 120 MET cc_start: 0.8993 (mmm) cc_final: 0.8311 (mmm) REVERT: E 125 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.9096 (mp10) REVERT: F 35 ARG cc_start: 0.9426 (ttp80) cc_final: 0.9207 (ttm110) REVERT: F 63 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8393 (mp0) REVERT: F 77 LYS cc_start: 0.9071 (mmtm) cc_final: 0.8808 (mmtm) REVERT: F 84 MET cc_start: 0.8254 (tpp) cc_final: 0.7943 (tpp) REVERT: F 92 ARG cc_start: 0.8771 (ttp80) cc_final: 0.8412 (ttp80) REVERT: H 47 GLN cc_start: 0.8798 (tt0) cc_final: 0.8502 (tm-30) REVERT: H 71 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8577 (tm-30) REVERT: H 93 GLU cc_start: 0.8935 (mp0) cc_final: 0.8604 (mp0) REVERT: H 116 LYS cc_start: 0.9051 (mmtt) cc_final: 0.8692 (mmtp) REVERT: L 63 LYS cc_start: 0.7460 (tptt) cc_final: 0.7199 (tppt) REVERT: C 73 ASN cc_start: 0.9343 (t0) cc_final: 0.9034 (t0) REVERT: C 90 ASP cc_start: 0.8564 (t70) cc_final: 0.8185 (t0) REVERT: G 57 TYR cc_start: 0.8679 (t80) cc_final: 0.8448 (t80) outliers start: 34 outliers final: 27 residues processed: 307 average time/residue: 0.3313 time to fit residues: 140.8753 Evaluate side-chains 305 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 276 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 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 94 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 77 optimal weight: 8.9990 chunk 88 optimal weight: 0.0270 chunk 120 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN E 68 GLN E 108 ASN H 49 HIS K 41 GLN ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS C 84 GLN C 94 ASN G 38 ASN G 68 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.081670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.057670 restraints weight = 76330.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.059401 restraints weight = 36483.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.060575 restraints weight = 23826.032| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 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 = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14865 Z= 0.175 Angle : 0.699 13.837 21349 Z= 0.384 Chirality : 0.038 0.201 2418 Planarity : 0.004 0.042 1690 Dihedral : 29.873 154.777 4321 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.31 % Allowed : 27.62 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 987 helix: 1.37 (0.20), residues: 624 sheet: 0.35 (0.96), residues: 29 loop : -1.19 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 61 HIS 0.006 0.001 HIS K 65 PHE 0.012 0.001 PHE E 67 TYR 0.026 0.002 TYR B 88 ARG 0.008 0.001 ARG K 67 Details of bonding type rmsd link_TRANS : bond 0.00037 ( 2) link_TRANS : angle 0.17047 ( 6) hydrogen bonds : bond 0.04233 ( 844) hydrogen bonds : angle 3.70380 ( 2154) metal coordination : bond 0.01095 ( 8) metal coordination : angle 6.60125 ( 9) covalent geometry : bond 0.00392 (14855) covalent geometry : angle 0.68593 (21334) *********************** 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 322 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 285 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8736 (tmm-80) cc_final: 0.8159 (tmm-80) REVERT: A 64 LYS cc_start: 0.9143 (tppp) cc_final: 0.8793 (tppp) REVERT: A 76 GLN cc_start: 0.8913 (pp30) cc_final: 0.8692 (pp30) REVERT: B 59 LYS cc_start: 0.9104 (tppt) cc_final: 0.8349 (tptp) REVERT: D 59 MET cc_start: 0.8738 (tpt) cc_final: 0.8499 (tpt) REVERT: E 90 MET cc_start: 0.8104 (mmt) cc_final: 0.7782 (mmp) REVERT: E 120 MET cc_start: 0.8990 (mmm) cc_final: 0.8325 (mmm) REVERT: F 63 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8403 (mp0) REVERT: F 77 LYS cc_start: 0.9066 (mmtm) cc_final: 0.8785 (mmtm) REVERT: F 84 MET cc_start: 0.8209 (tpp) cc_final: 0.7962 (tpp) REVERT: F 92 ARG cc_start: 0.8795 (ttp80) cc_final: 0.8243 (ttp80) REVERT: H 47 GLN cc_start: 0.8787 (tt0) cc_final: 0.8499 (tm-30) REVERT: H 71 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8599 (tm-30) REVERT: H 93 GLU cc_start: 0.8964 (mp0) cc_final: 0.8715 (mp0) REVERT: H 116 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8705 (mmtp) REVERT: K 46 LYS cc_start: 0.8997 (mmtt) cc_final: 0.8740 (mmtt) REVERT: L 63 LYS cc_start: 0.7510 (tptt) cc_final: 0.7243 (tppt) REVERT: C 56 GLU cc_start: 0.8901 (tp30) cc_final: 0.8470 (tp30) REVERT: C 73 ASN cc_start: 0.9356 (t0) cc_final: 0.9045 (t0) REVERT: C 90 ASP cc_start: 0.8569 (t70) cc_final: 0.8197 (t0) REVERT: G 57 TYR cc_start: 0.8720 (t80) cc_final: 0.8475 (t80) outliers start: 37 outliers final: 26 residues processed: 302 average time/residue: 0.3334 time to fit residues: 138.5842 Evaluate side-chains 301 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 274 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 B residue 96 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 49 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 83 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 35 optimal weight: 0.0060 chunk 71 optimal weight: 7.9990 chunk 50 optimal weight: 0.0040 chunk 18 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN D 109 HIS E 68 GLN ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN G 38 ASN G 68 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.082625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.058740 restraints weight = 75058.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.060479 restraints weight = 35847.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.061600 restraints weight = 23389.502| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14865 Z= 0.164 Angle : 0.702 14.095 21349 Z= 0.383 Chirality : 0.037 0.202 2418 Planarity : 0.004 0.043 1690 Dihedral : 29.820 154.938 4321 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.26 % Allowed : 28.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 987 helix: 1.35 (0.20), residues: 624 sheet: 0.50 (0.96), residues: 29 loop : -1.16 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 61 HIS 0.007 0.001 HIS K 65 PHE 0.012 0.001 PHE H 70 TYR 0.048 0.002 TYR D 83 ARG 0.008 0.001 ARG F 39 Details of bonding type rmsd link_TRANS : bond 0.00016 ( 2) link_TRANS : angle 0.10259 ( 6) hydrogen bonds : bond 0.04011 ( 844) hydrogen bonds : angle 3.64947 ( 2154) metal coordination : bond 0.00758 ( 8) metal coordination : angle 7.08272 ( 9) covalent geometry : bond 0.00364 (14855) covalent geometry : angle 0.68739 (21334) *********************** 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 314 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 286 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8431 (pp20) cc_final: 0.7638 (pp20) REVERT: A 53 ARG cc_start: 0.8760 (tmm-80) cc_final: 0.8204 (tmm-80) REVERT: A 64 LYS cc_start: 0.9112 (tppp) cc_final: 0.8803 (tppp) REVERT: A 76 GLN cc_start: 0.8918 (pp30) cc_final: 0.8692 (pp30) REVERT: B 59 LYS cc_start: 0.9100 (tppt) cc_final: 0.8278 (tptp) REVERT: B 88 TYR cc_start: 0.8553 (m-80) cc_final: 0.8169 (m-80) REVERT: D 109 HIS cc_start: 0.8081 (m-70) cc_final: 0.7329 (m170) REVERT: E 73 GLU cc_start: 0.8683 (tt0) cc_final: 0.8436 (tt0) REVERT: E 77 ASP cc_start: 0.8209 (m-30) cc_final: 0.7973 (m-30) REVERT: E 90 MET cc_start: 0.8066 (mmt) cc_final: 0.7748 (mmp) REVERT: E 108 ASN cc_start: 0.9119 (t0) cc_final: 0.8780 (t0) REVERT: E 120 MET cc_start: 0.8984 (mmm) cc_final: 0.8322 (mmm) REVERT: F 77 LYS cc_start: 0.9056 (mmtm) cc_final: 0.8758 (mmtm) REVERT: F 84 MET cc_start: 0.8211 (tpp) cc_final: 0.7873 (tpp) REVERT: F 92 ARG cc_start: 0.8767 (ttp80) cc_final: 0.8421 (ttp80) REVERT: H 47 GLN cc_start: 0.8754 (tt0) cc_final: 0.8470 (tm-30) REVERT: H 71 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8555 (tm-30) REVERT: H 93 GLU cc_start: 0.8968 (mp0) cc_final: 0.8705 (mp0) REVERT: H 116 LYS cc_start: 0.9051 (mmtt) cc_final: 0.8697 (mmtp) REVERT: K 46 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8727 (mmtt) REVERT: L 63 LYS cc_start: 0.7499 (tptt) cc_final: 0.7247 (tppt) REVERT: C 56 GLU cc_start: 0.8910 (tp30) cc_final: 0.8456 (tp30) REVERT: C 73 ASN cc_start: 0.9339 (t0) cc_final: 0.9039 (t0) REVERT: C 90 ASP cc_start: 0.8558 (t70) cc_final: 0.8195 (t0) REVERT: G 57 TYR cc_start: 0.8668 (t80) cc_final: 0.8441 (t80) outliers start: 28 outliers final: 23 residues processed: 298 average time/residue: 0.2966 time to fit residues: 122.0210 Evaluate side-chains 301 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 278 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 73 optimal weight: 6.9990 chunk 35 optimal weight: 0.1980 chunk 61 optimal weight: 7.9990 chunk 83 optimal weight: 0.0570 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN G 38 ASN G 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.081813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.057701 restraints weight = 86695.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.059546 restraints weight = 38925.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.060733 restraints weight = 24644.894| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 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 = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14865 Z= 0.184 Angle : 0.728 13.498 21349 Z= 0.396 Chirality : 0.038 0.202 2418 Planarity : 0.005 0.055 1690 Dihedral : 29.854 155.040 4321 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.91 % Allowed : 29.25 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.26), residues: 987 helix: 1.28 (0.20), residues: 624 sheet: 0.61 (0.94), residues: 28 loop : -1.20 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 61 HIS 0.007 0.001 HIS K 65 PHE 0.010 0.001 PHE E 67 TYR 0.098 0.002 TYR D 83 ARG 0.011 0.001 ARG K 67 Details of bonding type rmsd link_TRANS : bond 0.00049 ( 2) link_TRANS : angle 0.13622 ( 6) hydrogen bonds : bond 0.04368 ( 844) hydrogen bonds : angle 3.74514 ( 2154) metal coordination : bond 0.01141 ( 8) metal coordination : angle 6.85981 ( 9) covalent geometry : bond 0.00414 (14855) covalent geometry : angle 0.71409 (21334) ********************** 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 302 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 277 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8459 (pp20) cc_final: 0.7641 (pp20) REVERT: A 53 ARG cc_start: 0.8741 (tmm-80) cc_final: 0.8152 (tmm-80) REVERT: A 64 LYS cc_start: 0.9128 (tppp) cc_final: 0.8902 (tppp) REVERT: A 76 GLN cc_start: 0.8947 (pp30) cc_final: 0.8725 (pp30) REVERT: B 59 LYS cc_start: 0.9116 (tppt) cc_final: 0.8373 (tptp) REVERT: E 73 GLU cc_start: 0.8651 (tt0) cc_final: 0.8414 (tt0) REVERT: E 77 ASP cc_start: 0.8229 (m-30) cc_final: 0.7998 (m-30) REVERT: E 90 MET cc_start: 0.8085 (mmt) cc_final: 0.7774 (mmp) REVERT: E 120 MET cc_start: 0.8988 (mmm) cc_final: 0.8333 (mmm) REVERT: F 77 LYS cc_start: 0.9080 (mmtm) cc_final: 0.8828 (mmtm) REVERT: F 84 MET cc_start: 0.8233 (tpp) cc_final: 0.5761 (tpp) REVERT: F 92 ARG cc_start: 0.8831 (ttp80) cc_final: 0.8398 (ttp80) REVERT: H 47 GLN cc_start: 0.8776 (tt0) cc_final: 0.8482 (tm-30) REVERT: H 71 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8571 (tm-30) REVERT: H 93 GLU cc_start: 0.8977 (mp0) cc_final: 0.8696 (mp0) REVERT: H 116 LYS cc_start: 0.9060 (mmtt) cc_final: 0.8701 (mmtp) REVERT: K 46 LYS cc_start: 0.8925 (mmtt) cc_final: 0.8708 (mmtt) REVERT: L 63 LYS cc_start: 0.7527 (tptt) cc_final: 0.7266 (tppt) REVERT: C 36 LYS cc_start: 0.9260 (pttt) cc_final: 0.9034 (ptmm) REVERT: C 56 GLU cc_start: 0.8914 (tp30) cc_final: 0.8465 (tp30) REVERT: C 63 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9227 (mm) REVERT: C 90 ASP cc_start: 0.8546 (t70) cc_final: 0.8215 (t0) REVERT: G 57 TYR cc_start: 0.8716 (t80) cc_final: 0.8494 (t80) outliers start: 25 outliers final: 23 residues processed: 288 average time/residue: 0.3553 time to fit residues: 143.0963 Evaluate side-chains 293 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 269 time to evaluate : 2.150 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 22 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 83 optimal weight: 0.0020 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN D 109 HIS E 68 GLN ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 68 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.080776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.056957 restraints weight = 70893.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.058637 restraints weight = 35250.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.059714 restraints weight = 23484.264| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 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 = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14865 Z= 0.216 Angle : 0.747 13.806 21349 Z= 0.409 Chirality : 0.039 0.248 2418 Planarity : 0.005 0.053 1690 Dihedral : 29.964 153.863 4321 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.38 % Allowed : 28.79 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 987 helix: 1.20 (0.21), residues: 622 sheet: 0.58 (0.94), residues: 28 loop : -1.34 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.005 TRP K 77 HIS 0.007 0.001 HIS K 65 PHE 0.010 0.001 PHE H 70 TYR 0.124 0.003 TYR D 83 ARG 0.009 0.001 ARG K 67 Details of bonding type rmsd link_TRANS : bond 0.00101 ( 2) link_TRANS : angle 0.22640 ( 6) hydrogen bonds : bond 0.04791 ( 844) hydrogen bonds : angle 3.86276 ( 2154) metal coordination : bond 0.01689 ( 8) metal coordination : angle 6.63649 ( 9) covalent geometry : bond 0.00483 (14855) covalent geometry : angle 0.73472 (21334) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6745.23 seconds wall clock time: 120 minutes 26.20 seconds (7226.20 seconds total)