Starting phenix.real_space_refine on Fri Jul 3 12:20:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vg1_43197/07_2026/8vg1_43197.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vg1_43197/07_2026/8vg1_43197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vg1_43197/07_2026/8vg1_43197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vg1_43197/07_2026/8vg1_43197.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vg1_43197/07_2026/8vg1_43197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vg1_43197/07_2026/8vg1_43197.map" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 1 6.06 5 P 342 5.49 5 S 27 5.16 5 C 8022 2.51 5 N 2688 2.21 5 O 3354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14434 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3501 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "J" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3510 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "O" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 856 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain: "T" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 414 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14039 SG CYS T 271 25.471 18.700 101.461 1.00183.13 S ATOM 14058 SG CYS T 274 24.780 19.674 105.145 1.00185.68 S ATOM 14201 SG CYS T 292 28.170 20.609 103.380 1.00170.07 S ATOM 14220 SG CYS T 295 27.451 17.231 104.344 1.00173.94 S Time building chain proxies: 3.12, per 1000 atoms: 0.22 Number of scatterers: 14434 At special positions: 0 Unit cell: (92.928, 122.496, 180.576, 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 1 29.99 S 27 16.00 P 342 15.00 O 3354 8.00 N 2688 7.00 C 8022 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 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 491.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN T 501 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 295 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 292 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 271 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 274 " Number of angles added : 6 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1740 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 12 sheets defined 66.6% alpha, 3.3% beta 171 base pairs and 317 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.967A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.739A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.657A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.308A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.624A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.955A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.585A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.720A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.527A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.276A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.729A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 186 removed outlier: 3.517A pdb=" N ALA O 186 " --> pdb=" O ALA O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 193 through 204 Processing helix chain 'O' and resid 205 through 209 removed outlier: 3.893A pdb=" N GLN O 209 " --> pdb=" O TYR O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 225 Processing helix chain 'O' and resid 248 through 251 Processing helix chain 'T' and resid 292 through 303 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.916A 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 96 through 98 removed outlier: 6.646A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.137A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.729A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.136A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.091A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'O' and resid 191 through 192 removed outlier: 4.585A pdb=" N LEU O 191 " --> pdb=" O TRP O 244 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP O 244 " --> pdb=" O LEU O 191 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 283 through 284 450 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 417 hydrogen bonds 834 hydrogen bond angles 0 basepair planarities 171 basepair parallelities 317 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3009 1.33 - 1.45: 4676 1.45 - 1.57: 6991 1.57 - 1.69: 682 1.69 - 1.81: 43 Bond restraints: 15401 Sorted by residual: bond pdb=" C1' DT J 55 " pdb=" N1 DT J 55 " ideal model delta sigma weight residual 1.468 1.541 -0.073 1.40e-02 5.10e+03 2.75e+01 bond pdb=" C1' DT I 29 " pdb=" N1 DT I 29 " ideal model delta sigma weight residual 1.468 1.537 -0.069 1.40e-02 5.10e+03 2.40e+01 bond pdb=" C1' DC J 56 " pdb=" N1 DC J 56 " ideal model delta sigma weight residual 1.468 1.533 -0.065 1.40e-02 5.10e+03 2.18e+01 bond pdb=" C1' DT J 54 " pdb=" N1 DT J 54 " ideal model delta sigma weight residual 1.468 1.531 -0.063 1.40e-02 5.10e+03 1.99e+01 bond pdb=" C1' DC I 111 " pdb=" N1 DC I 111 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.99e+01 ... (remaining 15396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 19919 1.25 - 2.50: 1748 2.50 - 3.75: 542 3.75 - 5.01: 48 5.01 - 6.26: 4 Bond angle restraints: 22261 Sorted by residual: angle pdb=" O4' DA I 78 " pdb=" C1' DA I 78 " pdb=" N9 DA I 78 " ideal model delta sigma weight residual 108.00 111.32 -3.32 7.00e-01 2.04e+00 2.25e+01 angle pdb=" N3 DT I 71 " pdb=" C4 DT I 71 " pdb=" O4 DT I 71 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT I 121 " pdb=" C4 DT I 121 " pdb=" O4 DT I 121 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I 123 " pdb=" C4 DT I 123 " pdb=" O4 DT I 123 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT I 153 " pdb=" C4 DT I 153 " pdb=" O4 DT I 153 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 22256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.52: 6834 33.52 - 67.03: 1602 67.03 - 100.55: 31 100.55 - 134.07: 0 134.07 - 167.59: 2 Dihedral angle restraints: 8469 sinusoidal: 5771 harmonic: 2698 Sorted by residual: dihedral pdb=" C4' DG J 127 " pdb=" C3' DG J 127 " pdb=" O3' DG J 127 " pdb=" P DG J 128 " ideal model delta sinusoidal sigma weight residual 220.00 52.41 167.59 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DC J 93 " pdb=" C3' DC J 93 " pdb=" O3' DC J 93 " pdb=" P DC J 94 " ideal model delta sinusoidal sigma weight residual 220.00 63.87 156.13 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 163.63 16.37 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 8466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1696 0.039 - 0.079: 407 0.079 - 0.118: 137 0.118 - 0.158: 233 0.158 - 0.197: 34 Chirality restraints: 2507 Sorted by residual: chirality pdb=" C3' DT I 121 " pdb=" C4' DT I 121 " pdb=" O3' DT I 121 " pdb=" C2' DT I 121 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" C3' DC I 111 " pdb=" C4' DC I 111 " pdb=" O3' DC I 111 " pdb=" C2' DC I 111 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" C3' DA J 70 " pdb=" C4' DA J 70 " pdb=" O3' DA J 70 " pdb=" C2' DA J 70 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.01e-01 ... (remaining 2504 not shown) Planarity restraints: 1633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS O 237 " -0.043 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO O 238 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO O 238 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO O 238 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 131 " -0.035 2.00e-02 2.50e+03 1.45e-02 6.34e+00 pdb=" N9 DG I 131 " 0.031 2.00e-02 2.50e+03 pdb=" C8 DG I 131 " 0.009 2.00e-02 2.50e+03 pdb=" N7 DG I 131 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 131 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 131 " -0.007 2.00e-02 2.50e+03 pdb=" O6 DG I 131 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 131 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 131 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 131 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DG I 131 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 131 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 138 " -0.027 2.00e-02 2.50e+03 1.16e-02 4.02e+00 pdb=" N9 DG I 138 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DG I 138 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 138 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 138 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG I 138 " -0.000 2.00e-02 2.50e+03 pdb=" O6 DG I 138 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 138 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 138 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 138 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG I 138 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG I 138 " 0.008 2.00e-02 2.50e+03 ... (remaining 1630 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4211 2.86 - 3.37: 12501 3.37 - 3.88: 28858 3.88 - 4.39: 33533 4.39 - 4.90: 45718 Nonbonded interactions: 124821 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.351 3.040 nonbonded pdb=" OE2 GLU H 113 " pdb=" NH1 ARG T 320 " model vdw 2.371 3.120 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 78 " model vdw 2.375 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.377 3.040 nonbonded pdb=" N GLU A 59 " pdb=" OE1 GLU A 59 " model vdw 2.407 3.120 ... (remaining 124816 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' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 10 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.710 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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 : 0.007 0.073 15405 Z= 0.590 Angle : 0.824 8.079 22267 Z= 0.718 Chirality : 0.059 0.197 2507 Planarity : 0.005 0.064 1633 Dihedral : 26.205 167.585 6729 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.32 % Favored : 98.57 % Rotamer: Outliers : 0.51 % Allowed : 2.93 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.27), residues: 910 helix: 2.38 (0.21), residues: 588 sheet: -0.78 (1.29), residues: 12 loop : -0.25 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 49 TYR 0.010 0.001 TYR C 50 PHE 0.007 0.001 PHE F 61 TRP 0.014 0.001 TRP O 214 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.59 (15401) covalent geometry : angle 0.82059 / 0.72 (22261) hydrogen bonds : bond 0.09716 / 6.36 ( 867) hydrogen bonds : angle 3.37012 / 2.49 ( 2148) metal coordination : bond 0.01007 / 0.50 ( 4) metal coordination : angle 4.57506 / 2.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 185 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 31 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8408 (ttpt) REVERT: B 79 LYS cc_start: 0.8937 (mtpt) cc_final: 0.8552 (mtmt) REVERT: C 99 ARG cc_start: 0.8284 (mmp80) cc_final: 0.7988 (mmm-85) REVERT: D 59 MET cc_start: 0.9329 (tpp) cc_final: 0.9115 (tpp) REVERT: D 86 ARG cc_start: 0.8662 (mmt90) cc_final: 0.8447 (mmt90) REVERT: D 105 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8321 (mm-30) REVERT: D 113 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8599 (mm-30) REVERT: E 79 LYS cc_start: 0.8704 (tttp) cc_final: 0.8479 (ttpt) REVERT: E 90 MET cc_start: 0.8888 (mmm) cc_final: 0.8667 (mmp) REVERT: G 13 LYS cc_start: 0.8475 (tttp) cc_final: 0.8171 (tmtm) REVERT: G 41 GLU cc_start: 0.8520 (tt0) cc_final: 0.8239 (tt0) REVERT: G 95 LYS cc_start: 0.9240 (tmtm) cc_final: 0.9003 (tmtt) REVERT: H 37 TYR cc_start: 0.9482 (m-80) cc_final: 0.9218 (m-80) REVERT: H 47 GLN cc_start: 0.8712 (mt0) cc_final: 0.8420 (mt0) REVERT: H 59 MET cc_start: 0.9396 (tpp) cc_final: 0.9008 (tpp) REVERT: H 76 GLU cc_start: 0.8865 (tp30) cc_final: 0.8647 (tp30) REVERT: H 86 ARG cc_start: 0.8547 (mmt-90) cc_final: 0.8222 (mmt90) REVERT: H 105 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8515 (mm-30) REVERT: H 108 LYS cc_start: 0.8575 (mtpp) cc_final: 0.8233 (mttp) REVERT: O 181 MET cc_start: 0.8472 (tmm) cc_final: 0.8098 (ptt) REVERT: O 190 MET cc_start: 0.6002 (tpt) cc_final: 0.4846 (tpt) outliers start: 4 outliers final: 2 residues processed: 188 average time/residue: 0.9061 time to fit residues: 180.5119 Evaluate side-chains 163 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 161 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN D 63 ASN G 24 GLN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.127247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.076660 restraints weight = 22521.663| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.55 r_work: 0.2766 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15405 Z= 0.204 Angle : 0.694 8.054 22267 Z= 0.403 Chirality : 0.049 0.268 2507 Planarity : 0.005 0.069 1633 Dihedral : 30.351 171.735 4863 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.21 % Favored : 98.68 % Rotamer: Outliers : 1.40 % Allowed : 10.33 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.27), residues: 910 helix: 2.27 (0.20), residues: 603 sheet: -1.71 (1.11), residues: 12 loop : -0.06 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 36 TYR 0.012 0.002 TYR F 51 PHE 0.007 0.002 PHE E 67 TRP 0.017 0.002 TRP O 214 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.20 (15401) covalent geometry : angle 0.69232 / 0.40 (22261) hydrogen bonds : bond 0.05276 / 3.48 ( 867) hydrogen bonds : angle 3.06627 / 2.22 ( 2148) metal coordination : bond 0.00659 / 0.33 ( 4) metal coordination : angle 3.10109 / 1.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9058 (mtpt) cc_final: 0.8844 (mtmt) REVERT: C 73 ASN cc_start: 0.8651 (m-40) cc_final: 0.8373 (t160) REVERT: C 99 ARG cc_start: 0.8513 (mmp80) cc_final: 0.8087 (mmm-85) REVERT: D 105 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8458 (mm-30) REVERT: E 90 MET cc_start: 0.8943 (mmm) cc_final: 0.8705 (mmt) REVERT: G 13 LYS cc_start: 0.8494 (tttp) cc_final: 0.8196 (tmtm) REVERT: G 95 LYS cc_start: 0.9275 (tmtm) cc_final: 0.9038 (tmtt) REVERT: H 37 TYR cc_start: 0.9364 (m-80) cc_final: 0.9109 (m-80) REVERT: H 47 GLN cc_start: 0.8663 (mt0) cc_final: 0.8411 (mt0) REVERT: H 83 TYR cc_start: 0.8871 (m-10) cc_final: 0.8645 (m-10) REVERT: H 86 ARG cc_start: 0.8634 (mmt-90) cc_final: 0.8277 (mmt90) REVERT: H 105 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8771 (mm-30) REVERT: H 108 LYS cc_start: 0.8658 (mtpp) cc_final: 0.8271 (mttp) REVERT: O 190 MET cc_start: 0.6287 (tpt) cc_final: 0.4996 (tpt) outliers start: 11 outliers final: 4 residues processed: 167 average time/residue: 0.8889 time to fit residues: 157.1627 Evaluate side-chains 161 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 157 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 7 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 75 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 63 ASN T 302 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.123699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.072911 restraints weight = 22651.222| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.64 r_work: 0.2689 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 15405 Z= 0.383 Angle : 0.815 8.903 22267 Z= 0.447 Chirality : 0.056 0.269 2507 Planarity : 0.007 0.070 1633 Dihedral : 31.281 158.729 4861 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 1.91 % Allowed : 12.24 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.26), residues: 910 helix: 1.81 (0.20), residues: 599 sheet: -1.36 (1.21), residues: 12 loop : -0.31 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 262 TYR 0.015 0.002 TYR C 39 PHE 0.010 0.002 PHE D 70 TRP 0.018 0.002 TRP O 214 HIS 0.007 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00844 / 0.38 (15401) covalent geometry : angle 0.81251 / 0.45 (22261) hydrogen bonds : bond 0.07829 / 5.18 ( 867) hydrogen bonds : angle 3.33604 / 2.40 ( 2148) metal coordination : bond 0.00991 / 0.49 ( 4) metal coordination : angle 3.66905 / 1.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8873 (tt0) cc_final: 0.8643 (mt0) REVERT: C 13 LYS cc_start: 0.8967 (tptt) cc_final: 0.8761 (tptt) REVERT: C 99 ARG cc_start: 0.8632 (mmp80) cc_final: 0.8026 (mmm-85) REVERT: D 86 ARG cc_start: 0.8922 (mmt90) cc_final: 0.8628 (mmt180) REVERT: D 105 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8533 (mm-30) REVERT: E 90 MET cc_start: 0.9000 (mmm) cc_final: 0.8713 (mmt) REVERT: G 13 LYS cc_start: 0.8526 (tttp) cc_final: 0.8274 (tmtm) REVERT: G 95 LYS cc_start: 0.9282 (tmtm) cc_final: 0.9039 (tmtt) REVERT: H 33 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.6975 (mtp-110) REVERT: H 47 GLN cc_start: 0.8679 (mt0) cc_final: 0.8431 (mt0) REVERT: H 86 ARG cc_start: 0.8718 (mmt-90) cc_final: 0.8479 (mmt90) REVERT: H 108 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8371 (mttp) REVERT: O 190 MET cc_start: 0.6433 (tpt) cc_final: 0.5329 (tpt) outliers start: 15 outliers final: 7 residues processed: 158 average time/residue: 0.8533 time to fit residues: 143.0816 Evaluate side-chains 155 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.126564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.076020 restraints weight = 22616.493| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.55 r_work: 0.2756 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15405 Z= 0.142 Angle : 0.697 9.421 22267 Z= 0.390 Chirality : 0.049 0.255 2507 Planarity : 0.004 0.071 1633 Dihedral : 31.183 160.018 4861 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.32 % Favored : 98.57 % Rotamer: Outliers : 1.53 % Allowed : 13.65 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.27), residues: 910 helix: 2.26 (0.21), residues: 602 sheet: -1.57 (1.25), residues: 12 loop : -0.09 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O 262 TYR 0.012 0.002 TYR F 51 PHE 0.009 0.002 PHE E 67 TRP 0.013 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (15401) covalent geometry : angle 0.69532 / 0.39 (22261) hydrogen bonds : bond 0.04617 / 3.10 ( 867) hydrogen bonds : angle 3.00707 / 2.19 ( 2148) metal coordination : bond 0.00579 / 0.29 ( 4) metal coordination : angle 2.75672 / 1.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9082 (mtpt) cc_final: 0.8836 (mtmt) REVERT: C 99 ARG cc_start: 0.8599 (mmp80) cc_final: 0.7985 (mmm-85) REVERT: E 90 MET cc_start: 0.8993 (mmm) cc_final: 0.8764 (mmt) REVERT: F 25 ASN cc_start: 0.8802 (m110) cc_final: 0.8554 (m-40) REVERT: G 13 LYS cc_start: 0.8537 (tttp) cc_final: 0.8295 (tmtm) REVERT: G 95 LYS cc_start: 0.9277 (tmtm) cc_final: 0.9048 (tmtt) REVERT: H 33 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.6953 (mtp-110) REVERT: H 37 TYR cc_start: 0.9362 (m-80) cc_final: 0.9114 (m-80) REVERT: H 47 GLN cc_start: 0.8620 (mt0) cc_final: 0.8360 (mt0) REVERT: H 86 ARG cc_start: 0.8668 (mmt-90) cc_final: 0.8316 (mmt90) REVERT: H 108 LYS cc_start: 0.8669 (mtpp) cc_final: 0.8266 (mttp) REVERT: O 190 MET cc_start: 0.6302 (tpt) cc_final: 0.5108 (tpt) outliers start: 12 outliers final: 7 residues processed: 161 average time/residue: 0.8859 time to fit residues: 151.3658 Evaluate side-chains 161 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 153 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 55 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 50 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.126382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.076121 restraints weight = 22648.623| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.54 r_work: 0.2759 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15405 Z= 0.169 Angle : 0.659 7.822 22267 Z= 0.377 Chirality : 0.046 0.248 2507 Planarity : 0.004 0.072 1633 Dihedral : 30.979 160.847 4861 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.87 % Favored : 98.02 % Rotamer: Outliers : 1.91 % Allowed : 13.39 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.27), residues: 910 helix: 2.38 (0.21), residues: 602 sheet: -1.75 (1.34), residues: 12 loop : -0.01 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.015 0.001 TYR B 88 PHE 0.010 0.001 PHE A 67 TRP 0.012 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.17 (15401) covalent geometry : angle 0.65714 / 0.38 (22261) hydrogen bonds : bond 0.04680 / 3.12 ( 867) hydrogen bonds : angle 2.91420 / 2.11 ( 2148) metal coordination : bond 0.00481 / 0.24 ( 4) metal coordination : angle 2.92009 / 1.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8613 (ptpp) REVERT: B 79 LYS cc_start: 0.9081 (mtpt) cc_final: 0.8836 (mtpp) REVERT: C 99 ARG cc_start: 0.8578 (mmp80) cc_final: 0.7932 (mmm-85) REVERT: D 105 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8562 (mm-30) REVERT: E 90 MET cc_start: 0.8991 (mmm) cc_final: 0.8767 (mmp) REVERT: F 25 ASN cc_start: 0.8761 (m110) cc_final: 0.8528 (m-40) REVERT: G 13 LYS cc_start: 0.8546 (tttp) cc_final: 0.8288 (tmtm) REVERT: G 95 LYS cc_start: 0.9290 (tmtm) cc_final: 0.9032 (tmtt) REVERT: H 33 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.6970 (mtp-110) REVERT: H 47 GLN cc_start: 0.8651 (mt0) cc_final: 0.8417 (mt0) REVERT: H 83 TYR cc_start: 0.8813 (m-10) cc_final: 0.8507 (m-10) REVERT: H 86 ARG cc_start: 0.8664 (mmt-90) cc_final: 0.8336 (mmt90) REVERT: T 299 MET cc_start: 0.6814 (tpp) cc_final: 0.6582 (tmm) outliers start: 15 outliers final: 8 residues processed: 160 average time/residue: 0.8426 time to fit residues: 143.0265 Evaluate side-chains 162 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 101 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 106 optimal weight: 30.0000 chunk 115 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.126124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.075872 restraints weight = 22594.072| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.54 r_work: 0.2754 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15405 Z= 0.183 Angle : 0.668 12.120 22267 Z= 0.377 Chirality : 0.046 0.246 2507 Planarity : 0.004 0.072 1633 Dihedral : 31.050 161.478 4861 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 1.79 % Allowed : 13.90 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.27), residues: 910 helix: 2.38 (0.21), residues: 602 sheet: -1.57 (1.45), residues: 12 loop : 0.03 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 86 TYR 0.015 0.002 TYR B 88 PHE 0.011 0.002 PHE O 204 TRP 0.013 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (15401) covalent geometry : angle 0.66643 / 0.38 (22261) hydrogen bonds : bond 0.04609 / 3.06 ( 867) hydrogen bonds : angle 2.93371 / 2.14 ( 2148) metal coordination : bond 0.00559 / 0.28 ( 4) metal coordination : angle 2.75088 / 1.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9093 (mtpt) cc_final: 0.8810 (mtmt) REVERT: C 99 ARG cc_start: 0.8587 (mmp80) cc_final: 0.7944 (mmm-85) REVERT: D 105 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8559 (mm-30) REVERT: E 90 MET cc_start: 0.8991 (mmm) cc_final: 0.8757 (mmp) REVERT: F 25 ASN cc_start: 0.8746 (m110) cc_final: 0.8327 (m110) REVERT: F 92 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8291 (ttp80) REVERT: G 13 LYS cc_start: 0.8591 (tttp) cc_final: 0.8235 (tptp) REVERT: G 95 LYS cc_start: 0.9309 (tmtm) cc_final: 0.9057 (tmtt) REVERT: H 47 GLN cc_start: 0.8601 (mt0) cc_final: 0.8351 (mt0) REVERT: H 86 ARG cc_start: 0.8678 (mmt-90) cc_final: 0.8362 (mmt90) REVERT: H 108 LYS cc_start: 0.8631 (mtpm) cc_final: 0.8162 (mttp) REVERT: O 181 MET cc_start: 0.8604 (tmm) cc_final: 0.8173 (ptt) REVERT: O 190 MET cc_start: 0.6263 (tpt) cc_final: 0.5370 (tpt) REVERT: T 299 MET cc_start: 0.6837 (tpp) cc_final: 0.6588 (tmm) outliers start: 14 outliers final: 8 residues processed: 161 average time/residue: 0.8454 time to fit residues: 144.3707 Evaluate side-chains 161 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 55 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 9 optimal weight: 0.4980 chunk 115 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.126814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.076365 restraints weight = 22503.175| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.54 r_work: 0.2764 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15405 Z= 0.139 Angle : 0.660 11.369 22267 Z= 0.373 Chirality : 0.045 0.247 2507 Planarity : 0.004 0.073 1633 Dihedral : 31.043 161.205 4861 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.87 % Favored : 98.02 % Rotamer: Outliers : 1.79 % Allowed : 14.80 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.27), residues: 910 helix: 2.49 (0.21), residues: 602 sheet: -1.57 (1.44), residues: 12 loop : 0.08 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.014 0.001 TYR B 88 PHE 0.010 0.001 PHE A 67 TRP 0.012 0.002 TRP O 199 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (15401) covalent geometry : angle 0.65914 / 0.37 (22261) hydrogen bonds : bond 0.04374 / 2.91 ( 867) hydrogen bonds : angle 2.91799 / 2.12 ( 2148) metal coordination : bond 0.00490 / 0.24 ( 4) metal coordination : angle 2.50401 / 1.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9066 (mtpt) cc_final: 0.8786 (mtmt) REVERT: C 99 ARG cc_start: 0.8581 (mmp80) cc_final: 0.8104 (mmm160) REVERT: D 105 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8541 (mm-30) REVERT: F 25 ASN cc_start: 0.8719 (m110) cc_final: 0.8237 (m110) REVERT: F 92 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8240 (ttp80) REVERT: G 13 LYS cc_start: 0.8588 (tttp) cc_final: 0.8232 (tptp) REVERT: G 95 LYS cc_start: 0.9298 (tmtm) cc_final: 0.9041 (tmtt) REVERT: H 33 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6954 (mtp-110) REVERT: H 47 GLN cc_start: 0.8588 (mt0) cc_final: 0.8332 (mt0) REVERT: H 86 ARG cc_start: 0.8635 (mmt-90) cc_final: 0.8307 (mmt90) REVERT: H 108 LYS cc_start: 0.8620 (mtpm) cc_final: 0.8134 (mttp) REVERT: O 190 MET cc_start: 0.6215 (tpt) cc_final: 0.5338 (tpt) REVERT: T 299 MET cc_start: 0.6854 (tpp) cc_final: 0.6598 (tmm) outliers start: 14 outliers final: 8 residues processed: 155 average time/residue: 0.8732 time to fit residues: 143.5847 Evaluate side-chains 162 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 5 optimal weight: 0.5980 chunk 74 optimal weight: 30.0000 chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 63 optimal weight: 0.0270 chunk 114 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.126856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.076716 restraints weight = 22512.198| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.53 r_work: 0.2769 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15405 Z= 0.134 Angle : 0.656 10.911 22267 Z= 0.372 Chirality : 0.045 0.246 2507 Planarity : 0.004 0.073 1633 Dihedral : 31.030 161.429 4861 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 1.66 % Allowed : 15.18 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.27), residues: 910 helix: 2.50 (0.21), residues: 602 sheet: -1.54 (1.45), residues: 12 loop : 0.11 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 262 TYR 0.011 0.001 TYR B 88 PHE 0.010 0.001 PHE A 67 TRP 0.012 0.002 TRP O 199 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.13 (15401) covalent geometry : angle 0.65444 / 0.37 (22261) hydrogen bonds : bond 0.04276 / 2.85 ( 867) hydrogen bonds : angle 2.90491 / 2.11 ( 2148) metal coordination : bond 0.00400 / 0.20 ( 4) metal coordination : angle 2.41026 / 1.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8578 (ptpp) REVERT: B 79 LYS cc_start: 0.9064 (mtpt) cc_final: 0.8785 (mtmt) REVERT: C 99 ARG cc_start: 0.8572 (mmp80) cc_final: 0.8103 (mmm160) REVERT: D 105 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8538 (mm-30) REVERT: F 25 ASN cc_start: 0.8763 (m110) cc_final: 0.8550 (m-40) REVERT: F 92 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8237 (ttp80) REVERT: G 13 LYS cc_start: 0.8587 (tttp) cc_final: 0.8230 (tptp) REVERT: G 95 LYS cc_start: 0.9291 (tmtm) cc_final: 0.9032 (tmtt) REVERT: H 33 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.6952 (mtp-110) REVERT: H 47 GLN cc_start: 0.8579 (mt0) cc_final: 0.8337 (mt0) REVERT: H 86 ARG cc_start: 0.8631 (mmt-90) cc_final: 0.8308 (mmt90) REVERT: H 108 LYS cc_start: 0.8594 (mtpm) cc_final: 0.8111 (mttp) REVERT: O 181 MET cc_start: 0.8597 (tmm) cc_final: 0.8169 (ptt) REVERT: O 190 MET cc_start: 0.6193 (tpt) cc_final: 0.5238 (tpt) REVERT: T 299 MET cc_start: 0.6856 (tpp) cc_final: 0.6597 (tmm) outliers start: 13 outliers final: 9 residues processed: 157 average time/residue: 0.8665 time to fit residues: 144.0761 Evaluate side-chains 165 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Chi-restraints excluded: chain O residue 253 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 35 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.125709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.075346 restraints weight = 22656.772| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.55 r_work: 0.2744 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15405 Z= 0.208 Angle : 0.677 9.754 22267 Z= 0.381 Chirality : 0.047 0.256 2507 Planarity : 0.005 0.074 1633 Dihedral : 31.106 161.445 4861 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.98 % Favored : 97.91 % Rotamer: Outliers : 1.91 % Allowed : 14.92 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.27), residues: 910 helix: 2.36 (0.21), residues: 603 sheet: -1.38 (1.50), residues: 12 loop : 0.03 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 33 TYR 0.016 0.002 TYR B 88 PHE 0.010 0.002 PHE A 67 TRP 0.011 0.002 TRP O 199 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.21 (15401) covalent geometry : angle 0.67581 / 0.38 (22261) hydrogen bonds : bond 0.04949 / 3.28 ( 867) hydrogen bonds : angle 2.97911 / 2.16 ( 2148) metal coordination : bond 0.00591 / 0.29 ( 4) metal coordination : angle 2.58892 / 1.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 99 ARG cc_start: 0.8585 (mmp80) cc_final: 0.7967 (mmm-85) REVERT: D 86 ARG cc_start: 0.8851 (mmt-90) cc_final: 0.8577 (mmt90) REVERT: D 105 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8569 (mm-30) REVERT: F 25 ASN cc_start: 0.8767 (m110) cc_final: 0.8523 (m-40) REVERT: F 92 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8278 (ttp80) REVERT: G 13 LYS cc_start: 0.8614 (tttp) cc_final: 0.8260 (tptp) REVERT: G 95 LYS cc_start: 0.9297 (tmtm) cc_final: 0.9040 (tmtt) REVERT: H 33 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.6972 (mtp-110) REVERT: H 47 GLN cc_start: 0.8605 (mt0) cc_final: 0.8347 (mt0) REVERT: H 83 TYR cc_start: 0.8774 (m-10) cc_final: 0.8463 (m-10) REVERT: H 86 ARG cc_start: 0.8688 (mmt-90) cc_final: 0.8371 (mmt90) REVERT: H 108 LYS cc_start: 0.8617 (mtpm) cc_final: 0.8142 (mttp) REVERT: O 181 MET cc_start: 0.8592 (tmm) cc_final: 0.8173 (ptt) REVERT: O 190 MET cc_start: 0.6120 (tpt) cc_final: 0.5335 (tpt) REVERT: T 299 MET cc_start: 0.6857 (tpp) cc_final: 0.6633 (tmm) outliers start: 15 outliers final: 9 residues processed: 158 average time/residue: 0.8699 time to fit residues: 145.8077 Evaluate side-chains 161 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 115 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 112 optimal weight: 30.0000 chunk 87 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 40.0000 chunk 97 optimal weight: 9.9990 chunk 24 optimal weight: 0.0570 chunk 46 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 overall best weight: 2.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.124299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.073723 restraints weight = 22450.406| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.61 r_work: 0.2711 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 15405 Z= 0.297 Angle : 0.745 10.334 22267 Z= 0.408 Chirality : 0.051 0.266 2507 Planarity : 0.005 0.074 1633 Dihedral : 31.405 161.219 4861 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.20 % Favored : 97.69 % Rotamer: Outliers : 1.91 % Allowed : 15.43 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.27), residues: 910 helix: 2.08 (0.20), residues: 603 sheet: -1.44 (1.46), residues: 12 loop : -0.17 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 33 TYR 0.017 0.002 TYR B 88 PHE 0.010 0.002 PHE O 204 TRP 0.010 0.002 TRP O 214 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.30 (15401) covalent geometry : angle 0.74387 / 0.41 (22261) hydrogen bonds : bond 0.06031 / 4.00 ( 867) hydrogen bonds : angle 3.15771 / 2.28 ( 2148) metal coordination : bond 0.00811 / 0.40 ( 4) metal coordination : angle 2.83209 / 1.48 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8631 (ptpp) REVERT: C 99 ARG cc_start: 0.8599 (mmp80) cc_final: 0.7981 (mmm-85) REVERT: D 105 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8573 (mm-30) REVERT: F 25 ASN cc_start: 0.8763 (m110) cc_final: 0.8520 (m-40) REVERT: F 92 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8228 (ttp80) REVERT: G 13 LYS cc_start: 0.8641 (tttp) cc_final: 0.8200 (tmtt) REVERT: G 95 LYS cc_start: 0.9277 (tmtm) cc_final: 0.9047 (tmtt) REVERT: H 33 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6965 (mtp-110) REVERT: H 47 GLN cc_start: 0.8622 (mt0) cc_final: 0.8359 (mt0) REVERT: H 86 ARG cc_start: 0.8716 (mmt-90) cc_final: 0.8433 (mmt90) REVERT: H 108 LYS cc_start: 0.8649 (mtpm) cc_final: 0.8170 (mttp) REVERT: O 190 MET cc_start: 0.6148 (tpt) cc_final: 0.5385 (tpt) REVERT: T 299 MET cc_start: 0.6872 (tpp) cc_final: 0.6667 (tmm) outliers start: 15 outliers final: 9 residues processed: 157 average time/residue: 0.8354 time to fit residues: 139.1899 Evaluate side-chains 161 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain O residue 201 MET Chi-restraints excluded: chain O residue 216 ASN Chi-restraints excluded: chain O residue 233 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 6.9990 chunk 56 optimal weight: 0.3980 chunk 94 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.125393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.075169 restraints weight = 22568.520| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.55 r_work: 0.2738 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15405 Z= 0.169 Angle : 0.714 11.225 22267 Z= 0.394 Chirality : 0.048 0.262 2507 Planarity : 0.005 0.074 1633 Dihedral : 31.405 160.350 4861 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.76 % Favored : 98.13 % Rotamer: Outliers : 1.53 % Allowed : 15.94 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.27), residues: 910 helix: 2.22 (0.21), residues: 603 sheet: -1.33 (1.49), residues: 12 loop : -0.09 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 33 TYR 0.016 0.002 TYR B 88 PHE 0.010 0.002 PHE E 67 TRP 0.010 0.002 TRP O 214 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (15401) covalent geometry : angle 0.71243 / 0.39 (22261) hydrogen bonds : bond 0.05156 / 3.44 ( 867) hydrogen bonds : angle 3.08952 / 2.24 ( 2148) metal coordination : bond 0.00655 / 0.32 ( 4) metal coordination : angle 2.57021 / 1.35 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6255.12 seconds wall clock time: 106 minutes 43.73 seconds (6403.73 seconds total)