Starting phenix.real_space_refine on Thu Sep 18 01:06:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vg0_43196/09_2025/8vg0_43196.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vg0_43196/09_2025/8vg0_43196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vg0_43196/09_2025/8vg0_43196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vg0_43196/09_2025/8vg0_43196.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vg0_43196/09_2025/8vg0_43196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vg0_43196/09_2025/8vg0_43196.map" } resolution = 3.07 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= 0.001 sd= 0.108 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 318 5.49 5 S 20 5.16 5 C 7214 2.51 5 N 2436 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 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13042 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3258 Classifications: {'DNA': 159} Link IDs: {'rna3p': 158} Chain: "J" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3261 Classifications: {'DNA': 159} Link IDs: {'rna3p': 158} 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: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 856 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} 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: "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 12647 SG CYS T 271 13.598 101.162 82.539 1.00310.47 S ATOM 12666 SG CYS T 274 13.084 100.826 78.752 1.00313.28 S ATOM 12809 SG CYS T 292 16.436 99.804 80.350 1.00287.96 S ATOM 12828 SG CYS T 295 15.448 103.401 80.082 1.00302.98 S Time building chain proxies: 3.23, per 1000 atoms: 0.25 Number of scatterers: 13042 At special positions: 0 Unit cell: (81.312, 121.44, 147.84, 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 20 16.00 P 318 15.00 O 3053 8.00 N 2436 7.00 C 7214 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: 1.09 Conformation dependent library (CDL) restraints added in 378.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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 274 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 271 " Number of angles added : 6 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1534 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 11 sheets defined 69.5% alpha, 2.7% beta 159 base pairs and 284 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.821A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (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: 3.534A 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: 3.700A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 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: 4.316A 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 124 removed outlier: 3.600A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.598A 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: 3.930A 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 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.699A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.306A 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 '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 104 through 124 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: 6.831A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.264A 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: 6.636A 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: 7.218A 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: 7.472A 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 'T' and resid 283 through 284 423 hydrogen bonds defined for protein. 1239 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 387 hydrogen bonds 774 hydrogen bond angles 0 basepair planarities 159 basepair parallelities 284 stacking parallelities Total time for adding SS restraints: 2.66 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 - 1.34: 2921 1.34 - 1.45: 4077 1.45 - 1.57: 6256 1.57 - 1.69: 634 1.69 - 1.81: 32 Bond restraints: 13920 Sorted by residual: bond pdb=" C1' DT J 55 " pdb=" N1 DT J 55 " ideal model delta sigma weight residual 1.490 1.544 -0.054 3.00e-02 1.11e+03 3.29e+00 bond pdb=" N ALA C 10 " pdb=" CA ALA C 10 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 bond pdb=" C3' DC J 93 " pdb=" O3' DC J 93 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.10e+00 bond pdb=" CA ASP F 24 " pdb=" CB ASP F 24 " ideal model delta sigma weight residual 1.528 1.553 -0.024 1.39e-02 5.18e+03 3.04e+00 bond pdb=" N LEU T 269 " pdb=" CA LEU T 269 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 ... (remaining 13915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 19589 2.15 - 4.30: 542 4.30 - 6.45: 23 6.45 - 8.60: 1 8.60 - 10.75: 1 Bond angle restraints: 20156 Sorted by residual: angle pdb=" CB MET T 299 " pdb=" CG MET T 299 " pdb=" SD MET T 299 " ideal model delta sigma weight residual 112.70 123.45 -10.75 3.00e+00 1.11e-01 1.28e+01 angle pdb=" CA MET T 299 " pdb=" CB MET T 299 " pdb=" CG MET T 299 " ideal model delta sigma weight residual 114.10 120.52 -6.42 2.00e+00 2.50e-01 1.03e+01 angle pdb=" C2' DT I 161 " pdb=" C1' DT I 161 " pdb=" N1 DT I 161 " ideal model delta sigma weight residual 113.50 118.10 -4.60 1.50e+00 4.44e-01 9.41e+00 angle pdb=" C2' DT I 69 " pdb=" C1' DT I 69 " pdb=" N1 DT I 69 " ideal model delta sigma weight residual 113.50 117.69 -4.19 1.50e+00 4.44e-01 7.81e+00 angle pdb=" C3' DC J 93 " pdb=" O3' DC J 93 " pdb=" P DC J 94 " ideal model delta sigma weight residual 120.20 124.38 -4.18 1.50e+00 4.44e-01 7.75e+00 ... (remaining 20151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.38: 6117 33.38 - 66.76: 1488 66.76 - 100.14: 40 100.14 - 133.53: 0 133.53 - 166.91: 2 Dihedral angle restraints: 7647 sinusoidal: 5268 harmonic: 2379 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 53.09 166.91 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 65.81 154.19 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CG ARG A 131 " pdb=" CD ARG A 131 " pdb=" NE ARG A 131 " pdb=" CZ ARG A 131 " ideal model delta sinusoidal sigma weight residual 180.00 135.09 44.91 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 7644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1463 0.029 - 0.058: 465 0.058 - 0.087: 291 0.087 - 0.116: 59 0.116 - 0.145: 12 Chirality restraints: 2290 Sorted by residual: chirality pdb=" P DC J 94 " pdb=" OP1 DC J 94 " pdb=" OP2 DC J 94 " pdb=" O5' DC J 94 " both_signs ideal model delta sigma weight residual True 2.35 -2.49 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA VAL T 304 " pdb=" N VAL T 304 " pdb=" C VAL T 304 " pdb=" CB VAL T 304 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 2287 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 83 " 0.001 2.00e-02 2.50e+03 1.50e-02 4.49e+00 pdb=" CG TYR D 83 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR D 83 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR D 83 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR D 83 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 83 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR D 83 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 83 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 131 " 0.026 2.00e-02 2.50e+03 1.13e-02 3.84e+00 pdb=" N9 DG I 131 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DG I 131 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 131 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DG I 131 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 131 " 0.006 2.00e-02 2.50e+03 pdb=" O6 DG I 131 " 0.008 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 " -0.003 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' DT I 161 " 0.022 2.00e-02 2.50e+03 1.15e-02 3.31e+00 pdb=" N1 DT I 161 " -0.026 2.00e-02 2.50e+03 pdb=" C2 DT I 161 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT I 161 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT I 161 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 161 " 0.004 2.00e-02 2.50e+03 pdb=" O4 DT I 161 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DT I 161 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 161 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT I 161 " 0.001 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 149 2.65 - 3.21: 10629 3.21 - 3.77: 24270 3.77 - 4.34: 31659 4.34 - 4.90: 44714 Nonbonded interactions: 111421 Sorted by model distance: nonbonded pdb=" OP1 DG J 103 " pdb=" OG SER D 32 " model vdw 2.082 3.040 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.110 3.040 nonbonded pdb=" OP1 DA I 144 " pdb=" OG SER H 32 " model vdw 2.141 3.040 nonbonded pdb=" OP1 DC I 53 " pdb=" NH1 ARG T 284 " model vdw 2.228 3.120 nonbonded pdb=" N GLU B 52 " pdb=" OE1 GLU B 52 " model vdw 2.230 3.120 ... (remaining 111416 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: 1.770 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.750 Find NCS groups from input model: 0.130 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13924 Z= 0.205 Angle : 0.710 10.746 20162 Z= 0.433 Chirality : 0.038 0.145 2290 Planarity : 0.004 0.037 1448 Dihedral : 27.185 166.908 6113 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % 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: 2.77 (0.29), residues: 805 helix: 2.64 (0.22), residues: 550 sheet: None (None), residues: 0 loop : 0.05 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 79 TYR 0.028 0.002 TYR D 83 PHE 0.005 0.001 PHE A 67 TRP 0.001 0.000 TRP T 282 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00478 (13920) covalent geometry : angle 0.70906 (20156) hydrogen bonds : bond 0.10245 ( 810) hydrogen bonds : angle 3.48845 ( 2013) metal coordination : bond 0.00312 ( 4) metal coordination : angle 1.82904 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7893 (pm20) cc_final: 0.7370 (pm20) REVERT: A 76 GLN cc_start: 0.8480 (tp40) cc_final: 0.8238 (tp40) REVERT: A 115 LYS cc_start: 0.8984 (mtmm) cc_final: 0.8773 (mtmm) REVERT: B 88 TYR cc_start: 0.7682 (m-10) cc_final: 0.7441 (m-10) REVERT: D 59 MET cc_start: 0.8795 (tpp) cc_final: 0.8586 (mmm) REVERT: D 83 TYR cc_start: 0.8038 (m-80) cc_final: 0.7518 (m-80) REVERT: H 86 ARG cc_start: 0.8390 (mmt-90) cc_final: 0.7162 (mmm160) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2020 time to fit residues: 36.7801 Evaluate side-chains 123 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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: 0.9980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 27 GLN F 75 HIS T 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.121169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.071096 restraints weight = 22168.552| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.31 r_work: 0.2736 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13924 Z= 0.207 Angle : 0.594 6.984 20162 Z= 0.359 Chirality : 0.036 0.136 2290 Planarity : 0.004 0.038 1448 Dihedral : 30.316 179.709 4473 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.61 % Allowed : 8.91 % Favored : 89.49 % 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: 2.89 (0.29), residues: 805 helix: 2.70 (0.21), residues: 561 sheet: None (None), residues: 0 loop : 0.02 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 11 TYR 0.036 0.002 TYR D 83 PHE 0.010 0.001 PHE A 67 TRP 0.001 0.000 TRP T 282 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00472 (13920) covalent geometry : angle 0.59246 (20156) hydrogen bonds : bond 0.04256 ( 810) hydrogen bonds : angle 2.83953 ( 2013) metal coordination : bond 0.00435 ( 4) metal coordination : angle 2.56389 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.8209 (mmm) cc_final: 0.7959 (mmm) REVERT: B 95 ARG cc_start: 0.8502 (mtp85) cc_final: 0.8264 (mtp85) REVERT: D 101 LEU cc_start: 0.8510 (mt) cc_final: 0.8273 (mt) REVERT: E 59 GLU cc_start: 0.8157 (pm20) cc_final: 0.7869 (pm20) outliers start: 11 outliers final: 6 residues processed: 136 average time/residue: 0.1827 time to fit residues: 32.1469 Evaluate side-chains 124 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 27 GLN F 93 GLN H 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.123355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.073712 restraints weight = 22430.803| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.92 r_work: 0.2813 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13924 Z= 0.231 Angle : 0.595 5.827 20162 Z= 0.359 Chirality : 0.036 0.139 2290 Planarity : 0.004 0.035 1448 Dihedral : 30.423 178.673 4473 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.04 % Allowed : 9.78 % Favored : 88.18 % 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: 2.78 (0.29), residues: 805 helix: 2.62 (0.21), residues: 560 sheet: None (None), residues: 0 loop : -0.03 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 35 TYR 0.015 0.002 TYR D 40 PHE 0.009 0.001 PHE A 67 TRP 0.001 0.000 TRP T 282 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00532 (13920) covalent geometry : angle 0.59392 (20156) hydrogen bonds : bond 0.04334 ( 810) hydrogen bonds : angle 2.84760 ( 2013) metal coordination : bond 0.00437 ( 4) metal coordination : angle 2.44141 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8771 (mtp85) cc_final: 0.8517 (mtp85) REVERT: D 35 GLU cc_start: 0.8511 (pt0) cc_final: 0.8195 (pt0) REVERT: E 59 GLU cc_start: 0.8472 (pm20) cc_final: 0.8087 (pm20) REVERT: E 120 MET cc_start: 0.8498 (mtt) cc_final: 0.8288 (mtt) REVERT: H 68 ASP cc_start: 0.9020 (t0) cc_final: 0.8711 (t0) REVERT: T 299 MET cc_start: 0.6516 (tmm) cc_final: 0.5717 (pmm) outliers start: 14 outliers final: 10 residues processed: 133 average time/residue: 0.1864 time to fit residues: 32.1036 Evaluate side-chains 128 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS B 27 GLN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.124940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.075332 restraints weight = 22211.910| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.98 r_work: 0.2835 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13924 Z= 0.171 Angle : 0.560 6.243 20162 Z= 0.342 Chirality : 0.034 0.133 2290 Planarity : 0.004 0.034 1448 Dihedral : 30.292 177.181 4473 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.61 % Allowed : 10.80 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.98 (0.29), residues: 805 helix: 2.79 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.02 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 35 TYR 0.016 0.001 TYR D 83 PHE 0.009 0.001 PHE A 67 TRP 0.001 0.000 TRP T 282 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00383 (13920) covalent geometry : angle 0.55887 (20156) hydrogen bonds : bond 0.03812 ( 810) hydrogen bonds : angle 2.66108 ( 2013) metal coordination : bond 0.00334 ( 4) metal coordination : angle 1.95947 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8332 (m-10) cc_final: 0.8062 (m-10) REVERT: D 35 GLU cc_start: 0.8485 (pt0) cc_final: 0.8141 (pt0) REVERT: D 83 TYR cc_start: 0.8404 (m-10) cc_final: 0.8203 (m-10) REVERT: D 93 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: E 59 GLU cc_start: 0.8331 (pm20) cc_final: 0.7945 (pm20) REVERT: E 120 MET cc_start: 0.8282 (mtt) cc_final: 0.8030 (mtt) outliers start: 11 outliers final: 10 residues processed: 132 average time/residue: 0.1897 time to fit residues: 32.3168 Evaluate side-chains 130 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 19 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 0.0270 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 103 optimal weight: 0.0870 chunk 94 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.126780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.077198 restraints weight = 22666.897| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.22 r_work: 0.2858 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13924 Z= 0.143 Angle : 0.542 9.514 20162 Z= 0.332 Chirality : 0.032 0.131 2290 Planarity : 0.003 0.033 1448 Dihedral : 29.994 173.870 4473 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.02 % Allowed : 12.55 % Favored : 86.42 % 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 aren not related in a simple way. whole: 3.32 (0.29), residues: 805 helix: 3.03 (0.21), residues: 561 sheet: None (None), residues: 0 loop : 0.20 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 35 TYR 0.013 0.001 TYR D 40 PHE 0.009 0.001 PHE A 67 TRP 0.000 0.000 TRP T 282 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00307 (13920) covalent geometry : angle 0.54102 (20156) hydrogen bonds : bond 0.03458 ( 810) hydrogen bonds : angle 2.45935 ( 2013) metal coordination : bond 0.00257 ( 4) metal coordination : angle 1.55353 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8301 (mtp85) cc_final: 0.7730 (mmt90) REVERT: C 13 LYS cc_start: 0.8975 (tptt) cc_final: 0.8667 (tppp) REVERT: D 35 GLU cc_start: 0.8424 (pt0) cc_final: 0.8035 (pt0) REVERT: D 59 MET cc_start: 0.8727 (tpp) cc_final: 0.8407 (mmm) REVERT: D 93 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: E 59 GLU cc_start: 0.7905 (pm20) cc_final: 0.7286 (pm20) REVERT: F 95 ARG cc_start: 0.8048 (mtp85) cc_final: 0.7667 (ttm-80) REVERT: T 299 MET cc_start: 0.7047 (tmm) cc_final: 0.6009 (pmm) outliers start: 7 outliers final: 3 residues processed: 131 average time/residue: 0.1930 time to fit residues: 32.5900 Evaluate side-chains 120 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 0.7980 chunk 73 optimal weight: 0.0170 chunk 62 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.126035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.076766 restraints weight = 22396.516| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.18 r_work: 0.2855 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13924 Z= 0.153 Angle : 0.543 8.307 20162 Z= 0.332 Chirality : 0.033 0.133 2290 Planarity : 0.003 0.033 1448 Dihedral : 30.076 173.419 4473 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.31 % Allowed : 13.43 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.37 (0.29), residues: 805 helix: 3.06 (0.21), residues: 561 sheet: None (None), residues: 0 loop : 0.22 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 35 TYR 0.018 0.001 TYR D 83 PHE 0.009 0.001 PHE A 67 TRP 0.001 0.000 TRP T 282 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00335 (13920) covalent geometry : angle 0.54271 (20156) hydrogen bonds : bond 0.03547 ( 810) hydrogen bonds : angle 2.49851 ( 2013) metal coordination : bond 0.00273 ( 4) metal coordination : angle 1.59301 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.7941 (m-10) cc_final: 0.7563 (m-10) REVERT: B 95 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7717 (mmt90) REVERT: C 13 LYS cc_start: 0.8962 (tptt) cc_final: 0.8675 (tppp) REVERT: D 35 GLU cc_start: 0.8401 (pt0) cc_final: 0.8004 (pt0) REVERT: D 83 TYR cc_start: 0.7982 (m-10) cc_final: 0.7610 (m-80) REVERT: D 93 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: E 59 GLU cc_start: 0.7864 (pm20) cc_final: 0.7378 (pm20) REVERT: F 95 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7718 (ttm-80) REVERT: T 299 MET cc_start: 0.7024 (tmm) cc_final: 0.6021 (pmm) outliers start: 9 outliers final: 5 residues processed: 124 average time/residue: 0.1851 time to fit residues: 29.7355 Evaluate side-chains 123 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.125112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.075701 restraints weight = 22404.795| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.18 r_work: 0.2840 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13924 Z= 0.165 Angle : 0.548 8.035 20162 Z= 0.334 Chirality : 0.033 0.137 2290 Planarity : 0.003 0.033 1448 Dihedral : 30.138 173.142 4473 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.17 % Allowed : 13.87 % Favored : 84.96 % 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: 3.34 (0.29), residues: 805 helix: 3.04 (0.21), residues: 561 sheet: None (None), residues: 0 loop : 0.18 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 35 TYR 0.015 0.001 TYR D 40 PHE 0.008 0.001 PHE A 67 TRP 0.001 0.000 TRP T 282 HIS 0.005 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00368 (13920) covalent geometry : angle 0.54709 (20156) hydrogen bonds : bond 0.03643 ( 810) hydrogen bonds : angle 2.53542 ( 2013) metal coordination : bond 0.00284 ( 4) metal coordination : angle 1.65807 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.7949 (m-10) cc_final: 0.7669 (m-10) REVERT: B 95 ARG cc_start: 0.8416 (mtp85) cc_final: 0.7833 (mmt90) REVERT: C 13 LYS cc_start: 0.8969 (tptt) cc_final: 0.8700 (tppp) REVERT: D 35 GLU cc_start: 0.8401 (pt0) cc_final: 0.7999 (pt0) REVERT: D 83 TYR cc_start: 0.8194 (m-10) cc_final: 0.7855 (m-10) REVERT: D 93 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: E 59 GLU cc_start: 0.7843 (pm20) cc_final: 0.7364 (pm20) REVERT: H 86 ARG cc_start: 0.8299 (mmt-90) cc_final: 0.7118 (mtm180) REVERT: T 299 MET cc_start: 0.7085 (tmm) cc_final: 0.6107 (pmm) outliers start: 8 outliers final: 5 residues processed: 125 average time/residue: 0.1905 time to fit residues: 30.6469 Evaluate side-chains 124 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 5.9990 chunk 105 optimal weight: 40.0000 chunk 40 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.124920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.075545 restraints weight = 22210.403| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.17 r_work: 0.2831 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13924 Z= 0.165 Angle : 0.558 9.495 20162 Z= 0.336 Chirality : 0.033 0.168 2290 Planarity : 0.003 0.034 1448 Dihedral : 30.132 172.625 4473 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.46 % Allowed : 13.28 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.32 (0.29), residues: 805 helix: 3.04 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.17 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 35 TYR 0.015 0.001 TYR D 40 PHE 0.009 0.001 PHE A 67 TRP 0.001 0.000 TRP T 282 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00369 (13920) covalent geometry : angle 0.55757 (20156) hydrogen bonds : bond 0.03660 ( 810) hydrogen bonds : angle 2.53837 ( 2013) metal coordination : bond 0.00281 ( 4) metal coordination : angle 1.62414 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8985 (tptt) cc_final: 0.8717 (tppp) REVERT: D 35 GLU cc_start: 0.8437 (pt0) cc_final: 0.8049 (pt0) REVERT: D 83 TYR cc_start: 0.8214 (m-10) cc_final: 0.7917 (m-10) REVERT: D 93 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: E 59 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7313 (pm20) REVERT: H 86 ARG cc_start: 0.8294 (mmt-90) cc_final: 0.7181 (mtm180) REVERT: T 299 MET cc_start: 0.7057 (tmm) cc_final: 0.6089 (pmm) outliers start: 10 outliers final: 6 residues processed: 126 average time/residue: 0.1833 time to fit residues: 30.0445 Evaluate side-chains 126 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 77 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.123859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.074769 restraints weight = 22477.317| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.89 r_work: 0.2830 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13924 Z= 0.212 Angle : 0.593 11.220 20162 Z= 0.352 Chirality : 0.035 0.171 2290 Planarity : 0.004 0.033 1448 Dihedral : 30.402 173.520 4473 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.31 % Allowed : 14.31 % Favored : 84.38 % 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: 3.11 (0.29), residues: 805 helix: 2.88 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.10 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 35 TYR 0.014 0.002 TYR D 83 PHE 0.008 0.001 PHE A 67 TRP 0.002 0.001 TRP T 282 HIS 0.005 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00487 (13920) covalent geometry : angle 0.59248 (20156) hydrogen bonds : bond 0.04090 ( 810) hydrogen bonds : angle 2.72013 ( 2013) metal coordination : bond 0.00380 ( 4) metal coordination : angle 1.96308 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: C 13 LYS cc_start: 0.9046 (tptt) cc_final: 0.8742 (tppp) REVERT: D 34 LYS cc_start: 0.9053 (pttm) cc_final: 0.8828 (pttm) REVERT: D 35 GLU cc_start: 0.8436 (pt0) cc_final: 0.8068 (pt0) REVERT: D 93 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: E 59 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7706 (pm20) REVERT: H 68 ASP cc_start: 0.9043 (t0) cc_final: 0.8745 (t0) REVERT: H 86 ARG cc_start: 0.8657 (mmt-90) cc_final: 0.7684 (mtm180) REVERT: T 299 MET cc_start: 0.7110 (tmm) cc_final: 0.6125 (pmm) outliers start: 9 outliers final: 7 residues processed: 130 average time/residue: 0.1854 time to fit residues: 31.2197 Evaluate side-chains 130 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 12 optimal weight: 4.9990 chunk 32 optimal weight: 0.1980 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN H 47 GLN H 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.124665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.075407 restraints weight = 22585.925| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.19 r_work: 0.2827 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13924 Z= 0.155 Angle : 0.564 11.031 20162 Z= 0.339 Chirality : 0.033 0.165 2290 Planarity : 0.003 0.035 1448 Dihedral : 30.143 172.071 4473 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.17 % Allowed : 14.60 % Favored : 84.23 % 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: 3.21 (0.29), residues: 805 helix: 2.95 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.14 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 35 TYR 0.029 0.002 TYR D 83 PHE 0.010 0.001 PHE A 67 TRP 0.001 0.000 TRP T 282 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00341 (13920) covalent geometry : angle 0.56370 (20156) hydrogen bonds : bond 0.03633 ( 810) hydrogen bonds : angle 2.56799 ( 2013) metal coordination : bond 0.00280 ( 4) metal coordination : angle 1.55996 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8453 (mtp85) cc_final: 0.8017 (ttm-80) REVERT: C 13 LYS cc_start: 0.8998 (tptt) cc_final: 0.8709 (tppp) REVERT: D 35 GLU cc_start: 0.8423 (pt0) cc_final: 0.8039 (pt0) REVERT: D 93 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: E 59 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7288 (pm20) REVERT: G 104 GLN cc_start: 0.9049 (mm110) cc_final: 0.8695 (mm110) REVERT: H 86 ARG cc_start: 0.8316 (mmt-90) cc_final: 0.7243 (mtm180) REVERT: T 299 MET cc_start: 0.7056 (tmm) cc_final: 0.6092 (pmm) outliers start: 8 outliers final: 5 residues processed: 129 average time/residue: 0.1781 time to fit residues: 30.0543 Evaluate side-chains 129 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 106 optimal weight: 0.0170 chunk 107 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 91 optimal weight: 0.0470 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.124987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.075876 restraints weight = 22419.848| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.17 r_work: 0.2839 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13924 Z= 0.152 Angle : 0.566 11.491 20162 Z= 0.340 Chirality : 0.033 0.164 2290 Planarity : 0.003 0.034 1448 Dihedral : 30.111 171.826 4473 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.17 % Allowed : 14.74 % Favored : 84.09 % 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: 3.17 (0.29), residues: 805 helix: 2.91 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.15 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 35 TYR 0.029 0.002 TYR D 83 PHE 0.010 0.001 PHE A 67 TRP 0.001 0.000 TRP T 282 HIS 0.005 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00333 (13920) covalent geometry : angle 0.56496 (20156) hydrogen bonds : bond 0.03641 ( 810) hydrogen bonds : angle 2.58646 ( 2013) metal coordination : bond 0.00291 ( 4) metal coordination : angle 1.59711 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3378.48 seconds wall clock time: 58 minutes 26.37 seconds (3506.37 seconds total)