Starting phenix.real_space_refine on Sat Aug 23 14:21:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6h_29769/08_2025/8g6h_29769.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6h_29769/08_2025/8g6h_29769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g6h_29769/08_2025/8g6h_29769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6h_29769/08_2025/8g6h_29769.map" model { file = "/net/cci-nas-00/data/ceres_data/8g6h_29769/08_2025/8g6h_29769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6h_29769/08_2025/8g6h_29769.cif" } resolution = 3.06 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= 0.002 sd= 0.017 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: 5 Type Number sf(0) Gaussians P 314 5.49 5 S 13 5.16 5 C 7171 2.51 5 N 2423 2.21 5 O 3053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12974 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 803 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MLY:plan-1': 1} Unresolved non-hydrogen planarities: 1 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: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MLY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3196 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "J" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3241 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "K" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LEU K 73 " occ=0.52 ... (6 atoms not shown) pdb=" CD2 LEU K 73 " occ=0.52 Time building chain proxies: 3.19, per 1000 atoms: 0.25 Number of scatterers: 12974 At special positions: 0 Unit cell: (124.696, 95.048, 133.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 P 314 15.00 O 3053 8.00 N 2423 7.00 C 7171 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: 0.65 Conformation dependent library (CDL) restraints added in 361.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 11 sheets defined 69.2% alpha, 5.1% beta 157 base pairs and 282 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.657A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.539A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.145A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.554A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.622A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.575A 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 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.789A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.623A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.510A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.083A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.590A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.584A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.569A pdb=" N MET H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.955A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 55 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.716A 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 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.092A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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 100 through 102 removed outlier: 6.804A 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: 6.774A 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: 6.968A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 'K' and resid 12 through 16 removed outlier: 8.988A pdb=" N LEU K 67 " --> pdb=" O GLN K 2 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE K 4 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU K 69 " --> pdb=" O PHE K 4 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS K 6 " --> pdb=" O LEU K 69 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU K 71 " --> pdb=" O LYS K 6 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 405 hydrogen bonds 810 hydrogen bond angles 0 basepair planarities 157 basepair parallelities 282 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 0.99 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: 2532 1.33 - 1.45: 4475 1.45 - 1.57: 6185 1.57 - 1.69: 626 1.69 - 1.81: 24 Bond restraints: 13842 Sorted by residual: bond pdb=" P DA J 16 " pdb=" OP2 DA J 16 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.45e+00 bond pdb=" P DG J 27 " pdb=" OP2 DG J 27 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.36e+00 bond pdb=" P DG J 27 " pdb=" OP1 DG J 27 " ideal model delta sigma weight residual 1.480 1.513 -0.033 2.00e-02 2.50e+03 2.70e+00 bond pdb=" P DA J 16 " pdb=" OP1 DA J 16 " ideal model delta sigma weight residual 1.480 1.512 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" CB GLN K 31 " pdb=" CG GLN K 31 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.55e+00 ... (remaining 13837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 19651 1.75 - 3.49: 372 3.49 - 5.24: 17 5.24 - 6.98: 8 6.98 - 8.73: 2 Bond angle restraints: 20050 Sorted by residual: angle pdb=" C3' DA J 26 " pdb=" O3' DA J 26 " pdb=" P DG J 27 " ideal model delta sigma weight residual 120.20 113.74 6.46 1.50e+00 4.44e-01 1.86e+01 angle pdb=" O3' DG J 27 " pdb=" P DA J 28 " pdb=" O5' DA J 28 " ideal model delta sigma weight residual 104.00 98.25 5.75 1.50e+00 4.44e-01 1.47e+01 angle pdb=" O3' DA J 16 " pdb=" P DA J 17 " pdb=" O5' DA J 17 " ideal model delta sigma weight residual 104.00 98.58 5.42 1.50e+00 4.44e-01 1.31e+01 angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DA J 16 " ideal model delta sigma weight residual 120.20 114.95 5.25 1.50e+00 4.44e-01 1.22e+01 angle pdb=" N ASP B 24 " pdb=" CA ASP B 24 " pdb=" CB ASP B 24 " ideal model delta sigma weight residual 113.65 109.16 4.49 1.47e+00 4.63e-01 9.35e+00 ... (remaining 20045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 5957 35.81 - 71.61: 1534 71.61 - 107.42: 11 107.42 - 143.23: 3 143.23 - 179.03: 1 Dihedral angle restraints: 7506 sinusoidal: 5116 harmonic: 2390 Sorted by residual: 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 40.97 179.03 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC I 4 " pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " pdb=" P DC I 5 " ideal model delta sinusoidal sigma weight residual 220.00 88.60 131.40 1 3.50e+01 8.16e-04 1.30e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 89.63 130.37 1 3.50e+01 8.16e-04 1.29e+01 ... (remaining 7503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2237 0.088 - 0.176: 52 0.176 - 0.264: 0 0.264 - 0.352: 0 0.352 - 0.440: 2 Chirality restraints: 2291 Sorted by residual: chirality pdb=" P DG J 27 " pdb=" OP1 DG J 27 " pdb=" OP2 DG J 27 " pdb=" O5' DG J 27 " both_signs ideal model delta sigma weight residual True 2.35 -2.79 -0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" P DA J 16 " pdb=" OP1 DA J 16 " pdb=" OP2 DA J 16 " pdb=" O5' DA J 16 " both_signs ideal model delta sigma weight residual True 2.35 -2.77 -0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 2288 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 24 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C ASP B 24 " 0.033 2.00e-02 2.50e+03 pdb=" O ASP B 24 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 25 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.025 2.00e-02 2.50e+03 1.05e-02 3.33e+00 pdb=" N9 DG I 47 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " -0.024 2.00e-02 2.50e+03 9.95e-03 2.97e+00 pdb=" N9 DG I 26 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " 0.002 2.00e-02 2.50e+03 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2198 2.78 - 3.31: 10604 3.31 - 3.84: 24244 3.84 - 4.37: 29377 4.37 - 4.90: 42149 Nonbonded interactions: 108572 Sorted by model distance: nonbonded pdb=" N GLU C 91 " pdb=" OE1 GLU C 91 " model vdw 2.254 3.120 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH1 ARG A 131 " model vdw 2.263 3.120 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.274 3.040 nonbonded pdb=" O GLN K 62 " pdb=" OG SER K 65 " model vdw 2.283 3.040 nonbonded pdb=" O GLU K 16 " pdb=" NZ LYS K 29 " model vdw 2.291 3.120 ... (remaining 108567 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' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.52 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.850 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13842 Z= 0.160 Angle : 0.562 8.726 20050 Z= 0.343 Chirality : 0.036 0.440 2291 Planarity : 0.004 0.037 1450 Dihedral : 28.192 179.033 5962 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 18.90 % Favored : 81.10 % 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 aren not related in a simple way. whole: 2.68 (0.30), residues: 800 helix: 2.65 (0.22), residues: 535 sheet: 1.95 (0.98), residues: 25 loop : -0.30 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.012 0.001 TYR F 51 PHE 0.009 0.001 PHE F 61 HIS 0.004 0.001 HIS K 68 Details of bonding type rmsd covalent geometry : bond 0.00327 (13842) covalent geometry : angle 0.56232 (20050) hydrogen bonds : bond 0.11614 ( 828) hydrogen bonds : angle 3.67302 ( 2046) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.337 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1539 time to fit residues: 25.2403 Evaluate side-chains 123 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 92 GLN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.119613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.085832 restraints weight = 21488.236| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.22 r_work: 0.2894 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.0680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13842 Z= 0.181 Angle : 0.524 6.498 20050 Z= 0.321 Chirality : 0.033 0.121 2291 Planarity : 0.004 0.036 1450 Dihedral : 30.106 179.563 4342 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.31 % Allowed : 17.88 % Favored : 80.81 % 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 aren not related in a simple way. whole: 3.10 (0.30), residues: 800 helix: 2.98 (0.22), residues: 543 sheet: 1.91 (1.03), residues: 26 loop : -0.27 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 72 TYR 0.007 0.001 TYR F 51 PHE 0.009 0.001 PHE F 61 HIS 0.004 0.001 HIS K 68 Details of bonding type rmsd covalent geometry : bond 0.00392 (13842) covalent geometry : angle 0.52365 (20050) hydrogen bonds : bond 0.05348 ( 828) hydrogen bonds : angle 2.86912 ( 2046) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.346 Fit side-chains REVERT: B 93 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.7338 (mp10) REVERT: C 64 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8213 (tt0) REVERT: C 73 ASN cc_start: 0.8154 (m-40) cc_final: 0.7902 (t0) REVERT: H 98 LEU cc_start: 0.9326 (mm) cc_final: 0.9076 (mm) outliers start: 9 outliers final: 4 residues processed: 129 average time/residue: 0.1676 time to fit residues: 28.5726 Evaluate side-chains 131 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.117862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.084069 restraints weight = 21626.372| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.18 r_work: 0.2861 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 13842 Z= 0.256 Angle : 0.556 6.723 20050 Z= 0.338 Chirality : 0.035 0.132 2291 Planarity : 0.004 0.039 1450 Dihedral : 30.165 177.064 4342 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.74 % Allowed : 17.59 % Favored : 80.67 % 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 aren not related in a simple way. whole: 2.93 (0.30), residues: 800 helix: 2.84 (0.22), residues: 543 sheet: 2.28 (1.05), residues: 25 loop : -0.38 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 55 TYR 0.008 0.001 TYR E 54 PHE 0.009 0.002 PHE F 61 HIS 0.004 0.001 HIS K 68 Details of bonding type rmsd covalent geometry : bond 0.00575 (13842) covalent geometry : angle 0.55576 (20050) hydrogen bonds : bond 0.06685 ( 828) hydrogen bonds : angle 2.92522 ( 2046) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.360 Fit side-chains REVERT: B 93 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7361 (mp10) REVERT: C 64 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: C 73 ASN cc_start: 0.8224 (m-40) cc_final: 0.7944 (t0) REVERT: E 131 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8928 (mtp85) REVERT: H 98 LEU cc_start: 0.9356 (mm) cc_final: 0.9118 (mm) outliers start: 12 outliers final: 8 residues processed: 130 average time/residue: 0.1700 time to fit residues: 29.0726 Evaluate side-chains 136 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 107 optimal weight: 30.0000 chunk 94 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.116840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.083154 restraints weight = 21574.186| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.19 r_work: 0.2837 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 13842 Z= 0.288 Angle : 0.577 5.508 20050 Z= 0.349 Chirality : 0.037 0.137 2291 Planarity : 0.004 0.041 1450 Dihedral : 30.436 176.308 4342 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.03 % Allowed : 17.59 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.73 (0.30), residues: 800 helix: 2.70 (0.22), residues: 542 sheet: 2.26 (1.14), residues: 23 loop : -0.45 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 55 TYR 0.009 0.001 TYR E 54 PHE 0.009 0.002 PHE H 67 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00654 (13842) covalent geometry : angle 0.57725 (20050) hydrogen bonds : bond 0.07115 ( 828) hydrogen bonds : angle 2.97371 ( 2046) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.300 Fit side-chains REVERT: B 93 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.7385 (mp10) REVERT: C 64 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: G 73 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7773 (t0) REVERT: H 98 LEU cc_start: 0.9352 (mm) cc_final: 0.9132 (mm) outliers start: 14 outliers final: 9 residues processed: 135 average time/residue: 0.1629 time to fit residues: 28.6770 Evaluate side-chains 140 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 112 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.118204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.085242 restraints weight = 21569.282| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.21 r_work: 0.2851 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13842 Z= 0.174 Angle : 0.560 12.083 20050 Z= 0.338 Chirality : 0.034 0.148 2291 Planarity : 0.004 0.037 1450 Dihedral : 30.452 176.858 4342 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.74 % Allowed : 18.17 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.88 (0.30), residues: 800 helix: 2.81 (0.22), residues: 542 sheet: 2.24 (1.15), residues: 23 loop : -0.36 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 71 TYR 0.010 0.001 TYR F 51 PHE 0.009 0.001 PHE F 61 HIS 0.003 0.001 HIS K 68 Details of bonding type rmsd covalent geometry : bond 0.00365 (13842) covalent geometry : angle 0.55960 (20050) hydrogen bonds : bond 0.06027 ( 828) hydrogen bonds : angle 2.96341 ( 2046) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.217 Fit side-chains REVERT: B 93 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7350 (mp10) REVERT: G 73 ASN cc_start: 0.8213 (t0) cc_final: 0.7639 (t0) REVERT: H 98 LEU cc_start: 0.9340 (mm) cc_final: 0.9086 (mm) REVERT: K 1 MET cc_start: 0.6172 (tmm) cc_final: 0.5396 (tmm) outliers start: 12 outliers final: 10 residues processed: 135 average time/residue: 0.1612 time to fit residues: 28.6560 Evaluate side-chains 138 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 101 optimal weight: 30.0000 chunk 58 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.117079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.083758 restraints weight = 21547.960| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.25 r_work: 0.2802 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 13842 Z= 0.269 Angle : 0.565 5.997 20050 Z= 0.343 Chirality : 0.036 0.133 2291 Planarity : 0.004 0.038 1450 Dihedral : 30.377 176.375 4342 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.89 % Allowed : 17.88 % Favored : 80.23 % 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 aren not related in a simple way. whole: 2.75 (0.30), residues: 800 helix: 2.75 (0.22), residues: 542 sheet: 0.82 (1.58), residues: 13 loop : -0.31 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 55 TYR 0.009 0.001 TYR E 54 PHE 0.009 0.002 PHE H 67 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00609 (13842) covalent geometry : angle 0.56525 (20050) hydrogen bonds : bond 0.06846 ( 828) hydrogen bonds : angle 2.92237 ( 2046) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.366 Fit side-chains REVERT: A 131 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.7932 (mtp180) REVERT: B 93 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7326 (mp10) REVERT: C 64 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: G 36 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8483 (mtpp) REVERT: G 73 ASN cc_start: 0.8123 (t0) cc_final: 0.7677 (t0) REVERT: H 98 LEU cc_start: 0.9332 (mm) cc_final: 0.9112 (mm) REVERT: K 1 MET cc_start: 0.6281 (tmm) cc_final: 0.5652 (tmm) outliers start: 13 outliers final: 8 residues processed: 133 average time/residue: 0.1703 time to fit residues: 29.5412 Evaluate side-chains 139 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 74 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.117969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.085032 restraints weight = 21465.295| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.19 r_work: 0.2847 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13842 Z= 0.181 Angle : 0.553 6.255 20050 Z= 0.336 Chirality : 0.034 0.157 2291 Planarity : 0.004 0.038 1450 Dihedral : 30.405 176.589 4342 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.18 % Allowed : 18.60 % Favored : 79.22 % 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 aren not related in a simple way. whole: 2.84 (0.30), residues: 800 helix: 2.82 (0.22), residues: 542 sheet: 0.83 (1.58), residues: 13 loop : -0.26 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 71 TYR 0.010 0.001 TYR F 51 PHE 0.008 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00386 (13842) covalent geometry : angle 0.55265 (20050) hydrogen bonds : bond 0.06135 ( 828) hydrogen bonds : angle 2.93095 ( 2046) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.363 Fit side-chains REVERT: A 131 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8040 (mtp180) REVERT: B 93 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7347 (mp10) REVERT: C 64 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: G 36 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8603 (mtpp) REVERT: G 73 ASN cc_start: 0.8141 (t0) cc_final: 0.7690 (t0) REVERT: H 98 LEU cc_start: 0.9349 (mm) cc_final: 0.9087 (mm) REVERT: K 1 MET cc_start: 0.6336 (tmm) cc_final: 0.5729 (tmm) outliers start: 15 outliers final: 11 residues processed: 133 average time/residue: 0.1707 time to fit residues: 29.8464 Evaluate side-chains 142 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 103 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.117921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.084707 restraints weight = 21492.425| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.21 r_work: 0.2825 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13842 Z= 0.206 Angle : 0.545 5.314 20050 Z= 0.332 Chirality : 0.034 0.126 2291 Planarity : 0.004 0.037 1450 Dihedral : 30.386 177.649 4342 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.74 % Allowed : 19.04 % Favored : 79.22 % 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 aren not related in a simple way. whole: 2.90 (0.30), residues: 800 helix: 2.87 (0.22), residues: 542 sheet: 0.85 (1.59), residues: 13 loop : -0.26 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 35 TYR 0.009 0.001 TYR F 51 PHE 0.009 0.001 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00454 (13842) covalent geometry : angle 0.54461 (20050) hydrogen bonds : bond 0.06048 ( 828) hydrogen bonds : angle 2.86185 ( 2046) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.318 Fit side-chains REVERT: A 131 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.7887 (mtp180) REVERT: B 93 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7312 (mp10) REVERT: C 64 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: G 36 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8490 (mtpp) REVERT: G 73 ASN cc_start: 0.8065 (t0) cc_final: 0.7635 (t0) REVERT: H 98 LEU cc_start: 0.9317 (mm) cc_final: 0.9073 (mm) REVERT: K 1 MET cc_start: 0.6196 (tmm) cc_final: 0.5636 (tmm) outliers start: 12 outliers final: 8 residues processed: 132 average time/residue: 0.1532 time to fit residues: 26.6087 Evaluate side-chains 139 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 27 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.117609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.084366 restraints weight = 21664.232| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.22 r_work: 0.2819 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13842 Z= 0.237 Angle : 0.551 5.570 20050 Z= 0.336 Chirality : 0.035 0.127 2291 Planarity : 0.004 0.037 1450 Dihedral : 30.340 177.156 4342 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.18 % Allowed : 18.31 % Favored : 79.51 % 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 aren not related in a simple way. whole: 2.86 (0.30), residues: 800 helix: 2.83 (0.22), residues: 542 sheet: 0.97 (1.60), residues: 13 loop : -0.28 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 55 TYR 0.009 0.001 TYR F 51 PHE 0.009 0.002 PHE F 61 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00532 (13842) covalent geometry : angle 0.55121 (20050) hydrogen bonds : bond 0.06306 ( 828) hydrogen bonds : angle 2.86286 ( 2046) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.253 Fit side-chains REVERT: A 131 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.7903 (mtp180) REVERT: B 93 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.7312 (mp10) REVERT: C 64 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: G 36 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8447 (mtpp) REVERT: G 73 ASN cc_start: 0.8053 (t0) cc_final: 0.7665 (t0) REVERT: H 98 LEU cc_start: 0.9325 (mm) cc_final: 0.9080 (mm) REVERT: K 1 MET cc_start: 0.6198 (tmm) cc_final: 0.5687 (tmm) outliers start: 15 outliers final: 10 residues processed: 134 average time/residue: 0.1439 time to fit residues: 25.4686 Evaluate side-chains 140 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.117659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.084325 restraints weight = 21541.629| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.15 r_work: 0.2869 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13842 Z= 0.227 Angle : 0.550 5.294 20050 Z= 0.335 Chirality : 0.035 0.144 2291 Planarity : 0.004 0.037 1450 Dihedral : 30.340 177.216 4342 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.03 % Allowed : 18.46 % Favored : 79.51 % 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 aren not related in a simple way. whole: 2.85 (0.30), residues: 800 helix: 2.83 (0.22), residues: 542 sheet: 0.95 (1.60), residues: 13 loop : -0.29 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 55 TYR 0.009 0.001 TYR F 51 PHE 0.009 0.002 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00508 (13842) covalent geometry : angle 0.55027 (20050) hydrogen bonds : bond 0.06256 ( 828) hydrogen bonds : angle 2.87268 ( 2046) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8020 (mtp180) REVERT: B 93 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7358 (mp10) REVERT: C 64 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: G 36 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8568 (mtpp) REVERT: G 73 ASN cc_start: 0.8114 (t0) cc_final: 0.7712 (t0) REVERT: H 98 LEU cc_start: 0.9349 (mm) cc_final: 0.9093 (mm) REVERT: K 1 MET cc_start: 0.6411 (tmm) cc_final: 0.5891 (tmm) outliers start: 14 outliers final: 10 residues processed: 133 average time/residue: 0.1704 time to fit residues: 29.8016 Evaluate side-chains 140 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.117942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.084880 restraints weight = 21494.827| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.11 r_work: 0.2881 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13842 Z= 0.188 Angle : 0.543 5.228 20050 Z= 0.331 Chirality : 0.033 0.140 2291 Planarity : 0.004 0.038 1450 Dihedral : 30.344 177.299 4342 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.47 % Allowed : 18.02 % Favored : 79.51 % 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 aren not related in a simple way. whole: 2.88 (0.30), residues: 800 helix: 2.86 (0.22), residues: 542 sheet: 0.95 (1.59), residues: 13 loop : -0.27 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 72 TYR 0.009 0.001 TYR F 51 PHE 0.009 0.001 PHE F 61 HIS 0.002 0.001 HIS K 68 Details of bonding type rmsd covalent geometry : bond 0.00407 (13842) covalent geometry : angle 0.54300 (20050) hydrogen bonds : bond 0.06108 ( 828) hydrogen bonds : angle 2.87118 ( 2046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3279.66 seconds wall clock time: 56 minutes 37.16 seconds (3397.16 seconds total)