Starting phenix.real_space_refine on Sun May 18 17:35:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u13_41800/05_2025/8u13_41800.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u13_41800/05_2025/8u13_41800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u13_41800/05_2025/8u13_41800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u13_41800/05_2025/8u13_41800.map" model { file = "/net/cci-nas-00/data/ceres_data/8u13_41800/05_2025/8u13_41800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u13_41800/05_2025/8u13_41800.cif" } resolution = 3.8 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 25 5.16 5 C 7139 2.51 5 N 2408 2.21 5 O 2958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12825 Number of models: 1 Model: "" Number of chains: 12 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: 737 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 735 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: "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 10617 SG CYS K 31 27.021 59.998 74.288 1.00394.38 S ATOM 10767 SG CYS K 51 26.391 63.713 73.415 1.00417.10 S ATOM 10791 SG CYS K 54 27.019 62.691 77.048 1.00421.64 S ATOM 10508 SG CYS K 16 19.411 66.329 66.379 1.00424.33 S ATOM 10526 SG CYS K 19 18.344 69.167 64.157 1.00433.92 S ATOM 10656 SG CYS K 36 20.356 66.435 62.624 1.00418.58 S ATOM 10678 SG CYS K 39 21.999 68.761 65.379 1.00418.47 S Time building chain proxies: 8.27, per 1000 atoms: 0.64 Number of scatterers: 12825 At special positions: 0 Unit cell: (103.788, 117.146, 117.146, 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 25 16.00 P 293 15.00 O 2958 8.00 N 2408 7.00 C 7139 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: 3.24 Conformation dependent library (CDL) restraints added in 1.1 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 16 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " Number of angles added : 9 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1612 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 11 sheets defined 68.9% alpha, 2.6% beta 141 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 7.47 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.756A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.685A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.498A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.528A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 56 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 removed outlier: 3.657A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.933A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.654A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'K' and resid 36 through 45 Processing helix chain 'K' and resid 58 through 68 removed outlier: 4.417A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 91 removed outlier: 4.140A pdb=" N ARG K 91 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.543A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.449A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.391A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.545A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98 removed outlier: 3.565A pdb=" N TYR F 98 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.296A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'K' and resid 27 through 28 removed outlier: 3.579A pdb=" N VAL K 27 " --> pdb=" O LEU K 35 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 432 hydrogen bonds defined for protein. 1273 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 359 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 5.09 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2525 1.33 - 1.45: 4369 1.45 - 1.57: 6137 1.57 - 1.69: 584 1.69 - 1.81: 36 Bond restraints: 13651 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.24e+00 bond pdb=" CG GLU B 63 " pdb=" CD GLU B 63 " ideal model delta sigma weight residual 1.516 1.480 0.036 2.50e-02 1.60e+03 2.05e+00 bond pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.80e+00 bond pdb=" CB ARG F 39 " pdb=" CG ARG F 39 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CG1 ILE G 62 " pdb=" CD1 ILE G 62 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.17e+00 ... (remaining 13646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 19055 1.60 - 3.20: 559 3.20 - 4.79: 49 4.79 - 6.39: 22 6.39 - 7.99: 7 Bond angle restraints: 19692 Sorted by residual: angle pdb=" N GLU B 63 " pdb=" CA GLU B 63 " pdb=" CB GLU B 63 " ideal model delta sigma weight residual 110.28 116.80 -6.52 1.55e+00 4.16e-01 1.77e+01 angle pdb=" C LEU B 62 " pdb=" N GLU B 63 " pdb=" CA GLU B 63 " ideal model delta sigma weight residual 120.31 114.63 5.68 1.52e+00 4.33e-01 1.40e+01 angle pdb=" CA GLU B 63 " pdb=" CB GLU B 63 " pdb=" CG GLU B 63 " ideal model delta sigma weight residual 114.10 120.77 -6.67 2.00e+00 2.50e-01 1.11e+01 angle pdb=" C SER H 112 " pdb=" N GLU H 113 " pdb=" CA GLU H 113 " ideal model delta sigma weight residual 121.14 115.58 5.56 1.75e+00 3.27e-01 1.01e+01 angle pdb=" C GLU E 50 " pdb=" CA GLU E 50 " pdb=" CB GLU E 50 " ideal model delta sigma weight residual 109.72 115.15 -5.43 1.92e+00 2.71e-01 8.00e+00 ... (remaining 19687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.48: 6095 34.48 - 68.96: 1363 68.96 - 103.44: 29 103.44 - 137.92: 0 137.92 - 172.40: 2 Dihedral angle restraints: 7489 sinusoidal: 4990 harmonic: 2499 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 151.88 28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ARG E 63 " pdb=" C ARG E 63 " pdb=" N LYS E 64 " pdb=" CA LYS E 64 " ideal model delta harmonic sigma weight residual -180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+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 47.60 172.40 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1866 0.045 - 0.091: 309 0.091 - 0.136: 61 0.136 - 0.181: 4 0.181 - 0.226: 1 Chirality restraints: 2241 Sorted by residual: chirality pdb=" CA GLU E 50 " pdb=" N GLU E 50 " pdb=" C GLU E 50 " pdb=" CB GLU E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE E 51 " pdb=" CA ILE E 51 " pdb=" CG1 ILE E 51 " pdb=" CG2 ILE E 51 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CA TYR E 54 " pdb=" N TYR E 54 " pdb=" C TYR E 54 " pdb=" CB TYR E 54 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 2238 not shown) Planarity restraints: 1477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 129 " 0.169 9.50e-02 1.11e+02 7.58e-02 3.72e+00 pdb=" NE ARG E 129 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG E 129 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG E 129 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 129 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 113 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" CD GLU H 113 " -0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU H 113 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU H 113 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 48 " 0.022 2.00e-02 2.50e+03 9.15e-03 2.51e+00 pdb=" N9 DG I 48 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DG I 48 " -0.008 2.00e-02 2.50e+03 pdb=" N7 DG I 48 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 48 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 48 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 48 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 48 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 48 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 48 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 48 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 48 " -0.002 2.00e-02 2.50e+03 ... (remaining 1474 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 483 2.70 - 3.25: 12231 3.25 - 3.80: 25255 3.80 - 4.35: 30112 4.35 - 4.90: 42904 Nonbonded interactions: 110985 Sorted by model distance: nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.145 3.120 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.153 2.496 nonbonded pdb=" OE1 GLU D 71 " pdb=" OH TYR C 39 " model vdw 2.180 3.040 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.240 3.040 nonbonded pdb=" NH2 ARG E 42 " pdb=" OP1 DG J -5 " model vdw 2.249 3.120 ... (remaining 110980 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 107 or resid 109 through 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 123)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 39.620 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 : 0.004 0.045 13661 Z= 0.163 Angle : 0.641 7.991 19707 Z= 0.368 Chirality : 0.036 0.226 2241 Planarity : 0.005 0.076 1475 Dihedral : 27.097 172.397 5871 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.28), residues: 842 helix: 1.16 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -0.84 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 61 HIS 0.004 0.001 HIS K 65 PHE 0.009 0.001 PHE G 25 TYR 0.021 0.002 TYR B 88 ARG 0.015 0.001 ARG C 99 Details of bonding type rmsd link_TRANS : bond 0.00262 ( 2) link_TRANS : angle 0.86790 ( 6) hydrogen bonds : bond 0.10747 ( 791) hydrogen bonds : angle 4.26585 ( 1987) metal coordination : bond 0.00645 ( 8) metal coordination : angle 3.29907 ( 9) covalent geometry : bond 0.00351 (13651) covalent geometry : angle 0.63756 (19692) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7092 (mt-10) REVERT: A 125 GLN cc_start: 0.9259 (mp10) cc_final: 0.8940 (mp10) REVERT: B 23 ARG cc_start: 0.8496 (mmp80) cc_final: 0.8126 (mmp80) REVERT: B 25 ASN cc_start: 0.8800 (m110) cc_final: 0.8440 (m110) REVERT: B 49 LEU cc_start: 0.9349 (pt) cc_final: 0.8356 (pt) REVERT: B 50 ILE cc_start: 0.9347 (tp) cc_final: 0.9047 (tp) REVERT: B 88 TYR cc_start: 0.8364 (m-80) cc_final: 0.8101 (m-80) REVERT: D 34 LYS cc_start: 0.8971 (mptt) cc_final: 0.8688 (mmtm) REVERT: D 57 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8600 (mmmm) REVERT: D 105 GLU cc_start: 0.8261 (tp30) cc_final: 0.7678 (tp30) REVERT: D 109 HIS cc_start: 0.8834 (m170) cc_final: 0.8628 (m170) REVERT: D 120 LYS cc_start: 0.9231 (tttp) cc_final: 0.8842 (ttmm) REVERT: E 53 ARG cc_start: 0.8788 (tmt-80) cc_final: 0.8330 (tmt-80) REVERT: E 54 TYR cc_start: 0.7863 (m-80) cc_final: 0.7639 (m-80) REVERT: E 57 SER cc_start: 0.7526 (p) cc_final: 0.6916 (p) REVERT: E 59 GLU cc_start: 0.8178 (pm20) cc_final: 0.7882 (pm20) REVERT: E 60 LEU cc_start: 0.8664 (mm) cc_final: 0.8015 (mm) REVERT: E 68 GLN cc_start: 0.8675 (pp30) cc_final: 0.8321 (pp30) REVERT: E 81 ASP cc_start: 0.8075 (m-30) cc_final: 0.7859 (m-30) REVERT: E 92 LEU cc_start: 0.9668 (mt) cc_final: 0.9462 (mt) REVERT: E 120 MET cc_start: 0.7832 (mtt) cc_final: 0.7405 (mtp) REVERT: E 125 GLN cc_start: 0.8554 (mp10) cc_final: 0.8001 (mp10) REVERT: F 49 LEU cc_start: 0.8913 (mm) cc_final: 0.8215 (mm) REVERT: H 68 ASP cc_start: 0.8399 (t70) cc_final: 0.8061 (t0) REVERT: H 83 TYR cc_start: 0.8409 (m-10) cc_final: 0.7681 (m-10) REVERT: C 84 GLN cc_start: 0.9172 (tm-30) cc_final: 0.8811 (tp-100) REVERT: G 61 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7763 (mm-30) REVERT: G 68 ASN cc_start: 0.8959 (m-40) cc_final: 0.8649 (m-40) REVERT: G 104 GLN cc_start: 0.8967 (mp10) cc_final: 0.8679 (mp10) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.2903 time to fit residues: 135.3749 Evaluate side-chains 289 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 30.0000 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 93 GLN E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN H 82 HIS H 84 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.074371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.049796 restraints weight = 78059.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.051392 restraints weight = 32961.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.052400 restraints weight = 21022.296| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13661 Z= 0.285 Angle : 0.695 8.479 19707 Z= 0.394 Chirality : 0.039 0.170 2241 Planarity : 0.005 0.037 1475 Dihedral : 30.325 173.205 4161 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.44 % Allowed : 17.47 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.67 (0.28), residues: 842 helix: 1.15 (0.21), residues: 587 sheet: None (None), residues: 0 loop : -1.14 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 77 HIS 0.007 0.001 HIS B 75 PHE 0.018 0.002 PHE H 65 TYR 0.023 0.002 TYR F 98 ARG 0.017 0.001 ARG G 29 Details of bonding type rmsd link_TRANS : bond 0.00154 ( 2) link_TRANS : angle 0.35454 ( 6) hydrogen bonds : bond 0.05788 ( 791) hydrogen bonds : angle 3.88525 ( 1987) metal coordination : bond 0.00897 ( 8) metal coordination : angle 4.60886 ( 9) covalent geometry : bond 0.00643 (13651) covalent geometry : angle 0.68868 (19692) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 283 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7124 (mp0) REVERT: A 125 GLN cc_start: 0.9441 (mp10) cc_final: 0.8932 (mp10) REVERT: B 23 ARG cc_start: 0.8662 (mmp80) cc_final: 0.8221 (mmp80) REVERT: B 25 ASN cc_start: 0.8876 (m110) cc_final: 0.8344 (m110) REVERT: B 63 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8353 (mp0) REVERT: B 88 TYR cc_start: 0.8879 (m-10) cc_final: 0.8495 (m-80) REVERT: D 34 LYS cc_start: 0.9023 (mptt) cc_final: 0.8777 (mmtm) REVERT: D 57 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8849 (mmmm) REVERT: D 79 ARG cc_start: 0.8341 (mtm110) cc_final: 0.7828 (mtm110) REVERT: D 105 GLU cc_start: 0.8545 (tp30) cc_final: 0.7295 (tp30) REVERT: D 109 HIS cc_start: 0.9209 (m170) cc_final: 0.8929 (m170) REVERT: D 120 LYS cc_start: 0.9260 (tttp) cc_final: 0.8894 (ttmm) REVERT: E 60 LEU cc_start: 0.8927 (mm) cc_final: 0.8423 (mm) REVERT: E 68 GLN cc_start: 0.8973 (pp30) cc_final: 0.8734 (pp30) REVERT: E 81 ASP cc_start: 0.8277 (m-30) cc_final: 0.8026 (m-30) REVERT: E 97 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8121 (mt-10) REVERT: E 120 MET cc_start: 0.7952 (mtt) cc_final: 0.7107 (mtt) REVERT: F 88 TYR cc_start: 0.8742 (m-10) cc_final: 0.7737 (m-10) REVERT: H 68 ASP cc_start: 0.9106 (t70) cc_final: 0.8718 (t0) REVERT: H 83 TYR cc_start: 0.8505 (m-10) cc_final: 0.7703 (m-10) REVERT: H 86 ARG cc_start: 0.9083 (tpp80) cc_final: 0.8846 (tpp80) REVERT: H 120 LYS cc_start: 0.9371 (ttmt) cc_final: 0.8853 (tptt) REVERT: C 24 GLN cc_start: 0.8594 (pm20) cc_final: 0.8296 (pm20) REVERT: C 78 ILE cc_start: 0.9022 (mm) cc_final: 0.8782 (mm) REVERT: C 84 GLN cc_start: 0.9296 (tm-30) cc_final: 0.8828 (tp-100) REVERT: C 91 GLU cc_start: 0.9275 (tp30) cc_final: 0.8915 (tp30) REVERT: C 92 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8150 (mp0) REVERT: G 104 GLN cc_start: 0.9263 (mp10) cc_final: 0.8848 (mp10) outliers start: 25 outliers final: 15 residues processed: 294 average time/residue: 0.3031 time to fit residues: 120.3017 Evaluate side-chains 285 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 269 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.0370 chunk 69 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 105 optimal weight: 0.0980 chunk 86 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS K 41 GLN C 73 ASN C 84 GLN C 89 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.077301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.053453 restraints weight = 64501.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.054718 restraints weight = 30612.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.055711 restraints weight = 20029.924| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13661 Z= 0.158 Angle : 0.636 9.135 19707 Z= 0.363 Chirality : 0.036 0.177 2241 Planarity : 0.004 0.038 1475 Dihedral : 29.956 173.123 4161 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.44 % Allowed : 21.18 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 842 helix: 1.30 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.12 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 77 HIS 0.023 0.001 HIS H 82 PHE 0.025 0.002 PHE E 67 TYR 0.025 0.002 TYR G 57 ARG 0.005 0.001 ARG D 99 Details of bonding type rmsd link_TRANS : bond 0.00044 ( 2) link_TRANS : angle 0.21620 ( 6) hydrogen bonds : bond 0.04260 ( 791) hydrogen bonds : angle 3.51060 ( 1987) metal coordination : bond 0.00645 ( 8) metal coordination : angle 4.43742 ( 9) covalent geometry : bond 0.00338 (13651) covalent geometry : angle 0.62952 (19692) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 312 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7546 (mt-10) REVERT: A 93 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7979 (tp40) REVERT: A 125 GLN cc_start: 0.9332 (mp10) cc_final: 0.8895 (mp10) REVERT: B 23 ARG cc_start: 0.8692 (mmp80) cc_final: 0.8197 (mmp80) REVERT: B 63 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8420 (mp0) REVERT: B 84 MET cc_start: 0.8638 (mmm) cc_final: 0.8346 (tpp) REVERT: B 88 TYR cc_start: 0.8723 (m-10) cc_final: 0.8465 (m-80) REVERT: D 34 LYS cc_start: 0.8994 (mptt) cc_final: 0.8708 (mmtm) REVERT: D 57 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8614 (mmmm) REVERT: D 79 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7774 (mtm110) REVERT: D 105 GLU cc_start: 0.8458 (tp30) cc_final: 0.7197 (tp30) REVERT: D 109 HIS cc_start: 0.9171 (m170) cc_final: 0.8851 (m170) REVERT: D 120 LYS cc_start: 0.9274 (tttp) cc_final: 0.8875 (ttmm) REVERT: E 60 LEU cc_start: 0.8846 (mm) cc_final: 0.8335 (mm) REVERT: E 68 GLN cc_start: 0.8802 (pp30) cc_final: 0.8482 (pp30) REVERT: E 81 ASP cc_start: 0.8229 (m-30) cc_final: 0.7944 (m-30) REVERT: E 97 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8180 (mt-10) REVERT: F 88 TYR cc_start: 0.8560 (m-10) cc_final: 0.7408 (m-10) REVERT: H 57 LYS cc_start: 0.9553 (mmmt) cc_final: 0.9346 (mmmm) REVERT: H 68 ASP cc_start: 0.8984 (t70) cc_final: 0.8678 (t0) REVERT: H 83 TYR cc_start: 0.8352 (m-10) cc_final: 0.7475 (m-10) REVERT: H 86 ARG cc_start: 0.9078 (tpp80) cc_final: 0.8747 (tpp80) REVERT: H 120 LYS cc_start: 0.9345 (ttmt) cc_final: 0.8826 (tptt) REVERT: C 78 ILE cc_start: 0.8962 (mm) cc_final: 0.8739 (mm) REVERT: C 84 GLN cc_start: 0.9359 (OUTLIER) cc_final: 0.9143 (tm-30) REVERT: C 91 GLU cc_start: 0.9298 (tp30) cc_final: 0.8906 (tp30) REVERT: C 92 GLU cc_start: 0.8849 (mt-10) cc_final: 0.7997 (mp0) REVERT: G 56 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8560 (tt0) REVERT: G 90 ASP cc_start: 0.8701 (t0) cc_final: 0.8146 (t0) REVERT: G 104 GLN cc_start: 0.9134 (mp10) cc_final: 0.8678 (mp10) outliers start: 25 outliers final: 11 residues processed: 316 average time/residue: 0.3004 time to fit residues: 126.8139 Evaluate side-chains 291 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 275 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 86 optimal weight: 30.0000 chunk 56 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS K 41 GLN C 73 ASN C 89 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.076157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.052529 restraints weight = 59034.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.054014 restraints weight = 28495.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.054955 restraints weight = 19207.905| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13661 Z= 0.188 Angle : 0.645 12.788 19707 Z= 0.366 Chirality : 0.036 0.191 2241 Planarity : 0.004 0.038 1475 Dihedral : 29.986 172.738 4161 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.71 % Allowed : 22.70 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 842 helix: 1.26 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.19 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 61 HIS 0.021 0.001 HIS H 82 PHE 0.019 0.002 PHE H 65 TYR 0.022 0.002 TYR G 57 ARG 0.006 0.001 ARG K 63 Details of bonding type rmsd link_TRANS : bond 0.00084 ( 2) link_TRANS : angle 0.23589 ( 6) hydrogen bonds : bond 0.04578 ( 791) hydrogen bonds : angle 3.54805 ( 1987) metal coordination : bond 0.00632 ( 8) metal coordination : angle 3.80903 ( 9) covalent geometry : bond 0.00421 (13651) covalent geometry : angle 0.63977 (19692) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 298 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7488 (mp0) REVERT: A 92 LEU cc_start: 0.9428 (mm) cc_final: 0.9228 (mm) REVERT: A 93 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8140 (tp40) REVERT: A 125 GLN cc_start: 0.9302 (mp10) cc_final: 0.8849 (mp10) REVERT: B 23 ARG cc_start: 0.8696 (mmp80) cc_final: 0.8199 (mmp80) REVERT: B 63 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8351 (mp0) REVERT: B 77 LYS cc_start: 0.9255 (mmtt) cc_final: 0.8437 (mmtt) REVERT: B 84 MET cc_start: 0.8664 (mmm) cc_final: 0.8205 (tpp) REVERT: B 88 TYR cc_start: 0.8725 (m-10) cc_final: 0.8412 (m-80) REVERT: D 34 LYS cc_start: 0.9029 (mptt) cc_final: 0.8734 (mmtm) REVERT: D 57 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8647 (mmmm) REVERT: D 76 GLU cc_start: 0.9273 (tp30) cc_final: 0.9019 (tp30) REVERT: D 79 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7789 (mtm110) REVERT: D 92 ARG cc_start: 0.8689 (ttp80) cc_final: 0.8050 (ttp80) REVERT: D 105 GLU cc_start: 0.8532 (tp30) cc_final: 0.7317 (tp30) REVERT: D 109 HIS cc_start: 0.9200 (m170) cc_final: 0.8880 (m170) REVERT: D 120 LYS cc_start: 0.9289 (tttp) cc_final: 0.8899 (ttmm) REVERT: E 60 LEU cc_start: 0.8909 (mm) cc_final: 0.8475 (mm) REVERT: E 68 GLN cc_start: 0.8910 (pp30) cc_final: 0.8653 (pp30) REVERT: E 81 ASP cc_start: 0.8132 (m-30) cc_final: 0.7859 (m-30) REVERT: E 97 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8182 (mt-10) REVERT: E 120 MET cc_start: 0.8021 (mtp) cc_final: 0.7578 (mtp) REVERT: F 88 TYR cc_start: 0.8570 (m-10) cc_final: 0.7423 (m-10) REVERT: H 68 ASP cc_start: 0.9043 (t70) cc_final: 0.8724 (t0) REVERT: H 83 TYR cc_start: 0.8330 (m-10) cc_final: 0.7361 (m-10) REVERT: H 86 ARG cc_start: 0.9062 (tpp80) cc_final: 0.8771 (tpp80) REVERT: H 120 LYS cc_start: 0.9343 (ttmt) cc_final: 0.8836 (tptt) REVERT: C 84 GLN cc_start: 0.9354 (tm-30) cc_final: 0.9024 (tp-100) REVERT: C 91 GLU cc_start: 0.9357 (tp30) cc_final: 0.8924 (tp30) REVERT: C 92 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8062 (mp0) REVERT: G 51 LEU cc_start: 0.9496 (tp) cc_final: 0.9127 (tt) REVERT: G 56 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8942 (tt0) REVERT: G 61 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8661 (mm-30) REVERT: G 90 ASP cc_start: 0.8849 (t0) cc_final: 0.8495 (t0) REVERT: G 104 GLN cc_start: 0.9196 (mp10) cc_final: 0.8732 (mp10) outliers start: 27 outliers final: 13 residues processed: 307 average time/residue: 0.2918 time to fit residues: 120.7264 Evaluate side-chains 295 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 278 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 82 optimal weight: 30.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS K 41 GLN C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.075740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.051443 restraints weight = 91878.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.053210 restraints weight = 35771.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.054313 restraints weight = 21741.644| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13661 Z= 0.193 Angle : 0.648 12.368 19707 Z= 0.366 Chirality : 0.037 0.154 2241 Planarity : 0.004 0.040 1475 Dihedral : 29.994 172.692 4161 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.54 % Allowed : 23.80 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.28), residues: 842 helix: 1.29 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.21 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 61 HIS 0.014 0.001 HIS H 82 PHE 0.015 0.002 PHE H 65 TYR 0.022 0.002 TYR H 40 ARG 0.008 0.000 ARG H 33 Details of bonding type rmsd link_TRANS : bond 0.00097 ( 2) link_TRANS : angle 0.25499 ( 6) hydrogen bonds : bond 0.04505 ( 791) hydrogen bonds : angle 3.53876 ( 1987) metal coordination : bond 0.00491 ( 8) metal coordination : angle 3.72296 ( 9) covalent geometry : bond 0.00435 (13651) covalent geometry : angle 0.64379 (19692) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 293 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7313 (mp0) REVERT: A 93 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8199 (tp40) REVERT: A 125 GLN cc_start: 0.9283 (mp10) cc_final: 0.8791 (mp10) REVERT: B 23 ARG cc_start: 0.8693 (mmp80) cc_final: 0.8255 (mmp80) REVERT: B 25 ASN cc_start: 0.8831 (m110) cc_final: 0.8196 (m110) REVERT: B 77 LYS cc_start: 0.9255 (mmtt) cc_final: 0.8499 (mmtt) REVERT: B 88 TYR cc_start: 0.8728 (m-10) cc_final: 0.8427 (m-80) REVERT: D 34 LYS cc_start: 0.9014 (mptt) cc_final: 0.8722 (mmtm) REVERT: D 57 LYS cc_start: 0.9094 (mmtt) cc_final: 0.8650 (mmmm) REVERT: D 76 GLU cc_start: 0.9293 (tp30) cc_final: 0.8929 (tp30) REVERT: D 79 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7904 (mtm110) REVERT: D 92 ARG cc_start: 0.8722 (ttp80) cc_final: 0.8038 (ttp80) REVERT: D 105 GLU cc_start: 0.8515 (tp30) cc_final: 0.7375 (tp30) REVERT: D 120 LYS cc_start: 0.9280 (tttp) cc_final: 0.8914 (ttmm) REVERT: E 60 LEU cc_start: 0.8917 (mm) cc_final: 0.8417 (mm) REVERT: E 68 GLN cc_start: 0.8942 (pp30) cc_final: 0.8650 (pp30) REVERT: E 120 MET cc_start: 0.8053 (mtp) cc_final: 0.7579 (mtp) REVERT: F 88 TYR cc_start: 0.8545 (m-10) cc_final: 0.7364 (m-10) REVERT: H 68 ASP cc_start: 0.9038 (t70) cc_final: 0.8737 (t0) REVERT: H 83 TYR cc_start: 0.8359 (m-10) cc_final: 0.7107 (m-10) REVERT: H 86 ARG cc_start: 0.9090 (tpp80) cc_final: 0.8819 (tpp80) REVERT: H 120 LYS cc_start: 0.9380 (ttmt) cc_final: 0.8883 (tptt) REVERT: C 38 ASN cc_start: 0.8322 (t0) cc_final: 0.8119 (t0) REVERT: C 84 GLN cc_start: 0.9259 (tm-30) cc_final: 0.8399 (tm-30) REVERT: C 91 GLU cc_start: 0.9372 (tp30) cc_final: 0.8926 (tp30) REVERT: C 92 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8101 (mp0) REVERT: G 90 ASP cc_start: 0.8894 (t0) cc_final: 0.8623 (t0) REVERT: G 104 GLN cc_start: 0.9191 (mp10) cc_final: 0.8729 (mp10) outliers start: 33 outliers final: 19 residues processed: 303 average time/residue: 0.2884 time to fit residues: 118.0524 Evaluate side-chains 299 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 278 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 55 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS H 109 HIS K 41 GLN C 73 ASN G 112 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.074463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.050018 restraints weight = 83660.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.051701 restraints weight = 34679.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.052732 restraints weight = 21842.986| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13661 Z= 0.258 Angle : 0.683 12.702 19707 Z= 0.386 Chirality : 0.039 0.184 2241 Planarity : 0.005 0.050 1475 Dihedral : 30.141 173.086 4161 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.50 % Allowed : 25.17 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.28), residues: 842 helix: 1.21 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.23 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 61 HIS 0.021 0.002 HIS H 82 PHE 0.013 0.002 PHE K 40 TYR 0.028 0.002 TYR G 57 ARG 0.006 0.001 ARG H 79 Details of bonding type rmsd link_TRANS : bond 0.00167 ( 2) link_TRANS : angle 0.31973 ( 6) hydrogen bonds : bond 0.05254 ( 791) hydrogen bonds : angle 3.73961 ( 1987) metal coordination : bond 0.00700 ( 8) metal coordination : angle 3.59427 ( 9) covalent geometry : bond 0.00585 (13651) covalent geometry : angle 0.67913 (19692) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 286 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8295 (tp40) REVERT: A 125 GLN cc_start: 0.9315 (mp10) cc_final: 0.8773 (mp10) REVERT: B 23 ARG cc_start: 0.8648 (mmp80) cc_final: 0.8175 (mmp80) REVERT: D 34 LYS cc_start: 0.9052 (mptt) cc_final: 0.8747 (mmtm) REVERT: D 57 LYS cc_start: 0.9131 (mmtt) cc_final: 0.8823 (mmmm) REVERT: D 76 GLU cc_start: 0.9307 (tp30) cc_final: 0.8914 (tp30) REVERT: D 79 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7811 (mtm110) REVERT: D 96 THR cc_start: 0.9547 (m) cc_final: 0.9323 (p) REVERT: D 105 GLU cc_start: 0.8628 (tp30) cc_final: 0.7576 (tp30) REVERT: D 120 LYS cc_start: 0.9301 (tttp) cc_final: 0.8942 (ttmm) REVERT: E 60 LEU cc_start: 0.8891 (mm) cc_final: 0.8249 (mm) REVERT: E 68 GLN cc_start: 0.9040 (pp30) cc_final: 0.8702 (pp30) REVERT: E 81 ASP cc_start: 0.8144 (m-30) cc_final: 0.7861 (m-30) REVERT: E 97 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8113 (mt-10) REVERT: E 120 MET cc_start: 0.8157 (mtp) cc_final: 0.7690 (mtp) REVERT: F 88 TYR cc_start: 0.8578 (m-10) cc_final: 0.7409 (m-10) REVERT: H 68 ASP cc_start: 0.9051 (t70) cc_final: 0.8713 (t0) REVERT: H 83 TYR cc_start: 0.8362 (m-10) cc_final: 0.7184 (m-10) REVERT: H 86 ARG cc_start: 0.9131 (tpp80) cc_final: 0.8900 (tpp80) REVERT: H 120 LYS cc_start: 0.9370 (ttmt) cc_final: 0.8852 (tptt) REVERT: C 38 ASN cc_start: 0.8435 (t0) cc_final: 0.8202 (t0) REVERT: C 84 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8821 (tm-30) REVERT: C 91 GLU cc_start: 0.9373 (tp30) cc_final: 0.8906 (tp30) REVERT: C 92 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8151 (mp0) REVERT: G 90 ASP cc_start: 0.8877 (t0) cc_final: 0.8536 (t0) REVERT: G 104 GLN cc_start: 0.9227 (mp10) cc_final: 0.8741 (mp10) outliers start: 40 outliers final: 23 residues processed: 300 average time/residue: 0.2777 time to fit residues: 113.4129 Evaluate side-chains 297 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 272 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 21 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS C 73 ASN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.074692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.050142 restraints weight = 83295.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.051806 restraints weight = 34425.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.052852 restraints weight = 21589.308| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13661 Z= 0.227 Angle : 0.691 13.394 19707 Z= 0.387 Chirality : 0.039 0.191 2241 Planarity : 0.004 0.048 1475 Dihedral : 30.102 173.088 4161 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.50 % Allowed : 27.24 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.28), residues: 842 helix: 1.27 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.27 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 61 HIS 0.020 0.002 HIS H 82 PHE 0.027 0.002 PHE E 67 TYR 0.026 0.002 TYR H 40 ARG 0.006 0.000 ARG C 99 Details of bonding type rmsd link_TRANS : bond 0.00126 ( 2) link_TRANS : angle 0.30926 ( 6) hydrogen bonds : bond 0.04857 ( 791) hydrogen bonds : angle 3.70639 ( 1987) metal coordination : bond 0.00664 ( 8) metal coordination : angle 3.95483 ( 9) covalent geometry : bond 0.00514 (13651) covalent geometry : angle 0.68563 (19692) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8320 (tp40) REVERT: A 105 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8426 (mm-30) REVERT: B 23 ARG cc_start: 0.8582 (mmp80) cc_final: 0.8120 (mmp80) REVERT: B 59 LYS cc_start: 0.9390 (ttmm) cc_final: 0.9048 (ttmm) REVERT: D 34 LYS cc_start: 0.9046 (mptt) cc_final: 0.8730 (mmtm) REVERT: D 57 LYS cc_start: 0.9116 (mmtt) cc_final: 0.8800 (mmmm) REVERT: D 96 THR cc_start: 0.9549 (m) cc_final: 0.9347 (p) REVERT: D 105 GLU cc_start: 0.8602 (tp30) cc_final: 0.7582 (tp30) REVERT: D 120 LYS cc_start: 0.9289 (tttp) cc_final: 0.8924 (ttmm) REVERT: E 60 LEU cc_start: 0.8814 (mm) cc_final: 0.8175 (mm) REVERT: E 68 GLN cc_start: 0.8995 (pp30) cc_final: 0.8647 (pp30) REVERT: E 97 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7999 (mt-10) REVERT: E 120 MET cc_start: 0.8131 (mtp) cc_final: 0.7676 (mtp) REVERT: F 88 TYR cc_start: 0.8554 (m-10) cc_final: 0.7485 (m-10) REVERT: H 68 ASP cc_start: 0.9080 (t70) cc_final: 0.8720 (t0) REVERT: H 83 TYR cc_start: 0.8474 (m-10) cc_final: 0.7179 (m-10) REVERT: H 85 LYS cc_start: 0.9525 (mptt) cc_final: 0.9310 (mmmm) REVERT: H 86 ARG cc_start: 0.9120 (tpp80) cc_final: 0.8880 (tpp80) REVERT: C 84 GLN cc_start: 0.9181 (tm-30) cc_final: 0.8800 (tm-30) REVERT: C 91 GLU cc_start: 0.9369 (tp30) cc_final: 0.8904 (tp30) REVERT: C 92 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8252 (mp0) REVERT: G 104 GLN cc_start: 0.9242 (mp10) cc_final: 0.8777 (mp10) outliers start: 40 outliers final: 26 residues processed: 289 average time/residue: 0.2886 time to fit residues: 112.9879 Evaluate side-chains 300 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 272 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 48 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS C 38 ASN C 68 ASN C 73 ASN G 112 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.076538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.052324 restraints weight = 105626.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.054025 restraints weight = 38272.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.055175 restraints weight = 22368.889| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13661 Z= 0.167 Angle : 0.682 12.295 19707 Z= 0.383 Chirality : 0.038 0.216 2241 Planarity : 0.005 0.049 1475 Dihedral : 29.903 171.808 4161 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.95 % Allowed : 28.34 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.28), residues: 842 helix: 1.28 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.28 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 61 HIS 0.020 0.001 HIS H 82 PHE 0.018 0.002 PHE E 67 TYR 0.022 0.002 TYR H 40 ARG 0.009 0.000 ARG D 92 Details of bonding type rmsd link_TRANS : bond 0.00062 ( 2) link_TRANS : angle 0.23673 ( 6) hydrogen bonds : bond 0.04261 ( 791) hydrogen bonds : angle 3.59820 ( 1987) metal coordination : bond 0.00605 ( 8) metal coordination : angle 3.43687 ( 9) covalent geometry : bond 0.00370 (13651) covalent geometry : angle 0.67789 (19692) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 293 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8343 (tp40) REVERT: A 105 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8423 (mm-30) REVERT: B 23 ARG cc_start: 0.8499 (mmp80) cc_final: 0.8111 (mmp80) REVERT: B 84 MET cc_start: 0.8372 (tpp) cc_final: 0.7951 (tpp) REVERT: D 34 LYS cc_start: 0.9030 (mptt) cc_final: 0.8738 (mmtm) REVERT: D 57 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8614 (mmmm) REVERT: D 59 MET cc_start: 0.9222 (tpp) cc_final: 0.8958 (tpp) REVERT: D 63 ASN cc_start: 0.9202 (t0) cc_final: 0.8958 (t0) REVERT: D 80 LEU cc_start: 0.9386 (tp) cc_final: 0.9182 (tp) REVERT: D 96 THR cc_start: 0.9481 (m) cc_final: 0.9262 (p) REVERT: D 105 GLU cc_start: 0.8577 (tp30) cc_final: 0.7633 (tp30) REVERT: D 120 LYS cc_start: 0.9225 (tttp) cc_final: 0.8870 (ttmm) REVERT: E 60 LEU cc_start: 0.8813 (mm) cc_final: 0.8360 (mm) REVERT: E 120 MET cc_start: 0.8031 (mtp) cc_final: 0.7589 (mtp) REVERT: F 88 TYR cc_start: 0.8513 (m-10) cc_final: 0.7448 (m-10) REVERT: H 68 ASP cc_start: 0.9047 (t70) cc_final: 0.8730 (t0) REVERT: H 83 TYR cc_start: 0.8491 (m-10) cc_final: 0.7158 (m-10) REVERT: H 85 LYS cc_start: 0.9491 (mptt) cc_final: 0.9258 (mmmm) REVERT: H 86 ARG cc_start: 0.9087 (tpp80) cc_final: 0.8831 (tpp80) REVERT: C 84 GLN cc_start: 0.9154 (tm-30) cc_final: 0.8628 (tm-30) REVERT: C 91 GLU cc_start: 0.9388 (tp30) cc_final: 0.8885 (tp30) REVERT: C 92 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8161 (mp0) REVERT: G 51 LEU cc_start: 0.9436 (tp) cc_final: 0.9210 (tp) REVERT: G 104 GLN cc_start: 0.9174 (mp10) cc_final: 0.8714 (mp10) outliers start: 36 outliers final: 21 residues processed: 307 average time/residue: 0.2813 time to fit residues: 118.2013 Evaluate side-chains 308 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 285 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 34 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS C 38 ASN C 73 ASN C 89 ASN G 112 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.077177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.052602 restraints weight = 94436.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.054196 restraints weight = 37233.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.055314 restraints weight = 22547.946| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13661 Z= 0.175 Angle : 0.702 12.691 19707 Z= 0.389 Chirality : 0.039 0.240 2241 Planarity : 0.004 0.051 1475 Dihedral : 29.875 171.339 4161 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.85 % Allowed : 29.57 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 842 helix: 1.18 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.27 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 61 HIS 0.015 0.001 HIS H 82 PHE 0.010 0.001 PHE H 70 TYR 0.026 0.002 TYR G 57 ARG 0.007 0.000 ARG D 92 Details of bonding type rmsd link_TRANS : bond 0.00072 ( 2) link_TRANS : angle 0.27670 ( 6) hydrogen bonds : bond 0.04399 ( 791) hydrogen bonds : angle 3.63625 ( 1987) metal coordination : bond 0.00599 ( 8) metal coordination : angle 3.14369 ( 9) covalent geometry : bond 0.00394 (13651) covalent geometry : angle 0.69952 (19692) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 284 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8025 (mt-10) REVERT: A 90 MET cc_start: 0.8966 (mmp) cc_final: 0.8666 (mmp) REVERT: A 93 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8260 (tp40) REVERT: A 105 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8406 (mm-30) REVERT: A 125 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8822 (mp10) REVERT: B 88 TYR cc_start: 0.8653 (m-80) cc_final: 0.8431 (m-80) REVERT: D 34 LYS cc_start: 0.8970 (mptt) cc_final: 0.8699 (mmtm) REVERT: D 57 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8623 (mmmm) REVERT: D 59 MET cc_start: 0.9215 (tpp) cc_final: 0.8948 (tpp) REVERT: D 76 GLU cc_start: 0.9150 (tp30) cc_final: 0.8859 (tp30) REVERT: D 79 ARG cc_start: 0.8631 (ttp-110) cc_final: 0.8388 (ttp-110) REVERT: D 92 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8082 (ttp80) REVERT: D 96 THR cc_start: 0.9462 (m) cc_final: 0.9229 (p) REVERT: D 105 GLU cc_start: 0.8531 (tp30) cc_final: 0.7551 (tp30) REVERT: D 120 LYS cc_start: 0.9197 (tttp) cc_final: 0.8855 (ttmm) REVERT: E 60 LEU cc_start: 0.8731 (mm) cc_final: 0.8187 (mp) REVERT: E 67 PHE cc_start: 0.9227 (t80) cc_final: 0.9017 (t80) REVERT: E 120 MET cc_start: 0.8092 (mtp) cc_final: 0.7650 (mtp) REVERT: F 88 TYR cc_start: 0.8580 (m-10) cc_final: 0.7551 (m-10) REVERT: H 68 ASP cc_start: 0.9047 (t70) cc_final: 0.8747 (t0) REVERT: H 83 TYR cc_start: 0.8522 (m-10) cc_final: 0.7136 (m-10) REVERT: H 85 LYS cc_start: 0.9501 (mptt) cc_final: 0.9274 (mmmm) REVERT: H 86 ARG cc_start: 0.9059 (tpp80) cc_final: 0.8810 (tpp80) REVERT: C 84 GLN cc_start: 0.9055 (tm-30) cc_final: 0.8172 (tm-30) REVERT: C 91 GLU cc_start: 0.9390 (tp30) cc_final: 0.8949 (tp30) REVERT: C 92 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8088 (mp0) REVERT: G 104 GLN cc_start: 0.9128 (mp10) cc_final: 0.8647 (mp10) outliers start: 28 outliers final: 18 residues processed: 295 average time/residue: 0.2992 time to fit residues: 121.1590 Evaluate side-chains 302 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 281 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN E 85 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.076251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.052487 restraints weight = 74995.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.053981 restraints weight = 32579.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.054945 restraints weight = 20684.246| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13661 Z= 0.200 Angle : 0.719 12.449 19707 Z= 0.398 Chirality : 0.039 0.281 2241 Planarity : 0.005 0.052 1475 Dihedral : 29.909 171.524 4161 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.89 % Allowed : 30.26 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.28), residues: 842 helix: 1.15 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.25 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 61 HIS 0.005 0.001 HIS B 75 PHE 0.023 0.002 PHE H 65 TYR 0.027 0.002 TYR G 57 ARG 0.012 0.001 ARG C 99 Details of bonding type rmsd link_TRANS : bond 0.00110 ( 2) link_TRANS : angle 0.31802 ( 6) hydrogen bonds : bond 0.04631 ( 791) hydrogen bonds : angle 3.66672 ( 1987) metal coordination : bond 0.00581 ( 8) metal coordination : angle 3.16575 ( 9) covalent geometry : bond 0.00454 (13651) covalent geometry : angle 0.71589 (19692) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 278 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8284 (tp40) REVERT: A 105 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8408 (mm-30) REVERT: A 125 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.8803 (mp10) REVERT: B 23 ARG cc_start: 0.8761 (mmp80) cc_final: 0.8261 (mmp80) REVERT: B 84 MET cc_start: 0.8282 (tpp) cc_final: 0.7976 (tpp) REVERT: B 88 TYR cc_start: 0.8704 (m-80) cc_final: 0.8405 (m-80) REVERT: D 34 LYS cc_start: 0.8951 (mptt) cc_final: 0.8643 (mmtm) REVERT: D 57 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8630 (mmmm) REVERT: D 76 GLU cc_start: 0.9143 (tp30) cc_final: 0.8781 (tp30) REVERT: D 79 ARG cc_start: 0.8662 (ttp-110) cc_final: 0.8331 (ttp-110) REVERT: D 92 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8072 (ttp80) REVERT: D 96 THR cc_start: 0.9488 (m) cc_final: 0.9261 (p) REVERT: D 105 GLU cc_start: 0.8528 (tp30) cc_final: 0.7614 (tp30) REVERT: D 120 LYS cc_start: 0.9214 (tttp) cc_final: 0.8873 (ttmm) REVERT: E 81 ASP cc_start: 0.8094 (m-30) cc_final: 0.7812 (m-30) REVERT: E 120 MET cc_start: 0.8113 (mtp) cc_final: 0.7692 (mtp) REVERT: F 88 TYR cc_start: 0.8631 (m-10) cc_final: 0.7754 (m-10) REVERT: H 68 ASP cc_start: 0.9029 (t70) cc_final: 0.8716 (t0) REVERT: H 83 TYR cc_start: 0.8572 (m-10) cc_final: 0.7336 (m-10) REVERT: H 85 LYS cc_start: 0.9508 (mptt) cc_final: 0.9272 (mmmm) REVERT: H 86 ARG cc_start: 0.9060 (tpp80) cc_final: 0.8805 (tpp80) REVERT: C 39 TYR cc_start: 0.8640 (m-80) cc_final: 0.8391 (m-80) REVERT: C 64 GLU cc_start: 0.8787 (tt0) cc_final: 0.8245 (tm-30) REVERT: C 84 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8640 (tm-30) REVERT: C 91 GLU cc_start: 0.9393 (tp30) cc_final: 0.8952 (tp30) REVERT: C 92 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8109 (mp0) REVERT: G 104 GLN cc_start: 0.9131 (mp10) cc_final: 0.8649 (mp10) outliers start: 21 outliers final: 15 residues processed: 287 average time/residue: 0.2871 time to fit residues: 112.3837 Evaluate side-chains 294 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 276 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 73 ASN C 89 ASN G 112 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.077482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.053262 restraints weight = 85818.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.055017 restraints weight = 34438.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.056086 restraints weight = 21096.660| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13661 Z= 0.173 Angle : 0.723 13.595 19707 Z= 0.397 Chirality : 0.039 0.299 2241 Planarity : 0.005 0.051 1475 Dihedral : 29.853 171.031 4161 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.30 % Allowed : 30.54 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 842 helix: 1.03 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.23 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 61 HIS 0.004 0.001 HIS F 75 PHE 0.022 0.002 PHE H 65 TYR 0.023 0.002 TYR G 57 ARG 0.007 0.000 ARG D 92 Details of bonding type rmsd link_TRANS : bond 0.00062 ( 2) link_TRANS : angle 0.28844 ( 6) hydrogen bonds : bond 0.04375 ( 791) hydrogen bonds : angle 3.63098 ( 1987) metal coordination : bond 0.00593 ( 8) metal coordination : angle 3.08418 ( 9) covalent geometry : bond 0.00385 (13651) covalent geometry : angle 0.72048 (19692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4898.34 seconds wall clock time: 85 minutes 59.53 seconds (5159.53 seconds total)