Starting phenix.real_space_refine on Sat Jan 18 21:07:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vg0_43196/01_2025/8vg0_43196.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vg0_43196/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vg0_43196/01_2025/8vg0_43196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vg0_43196/01_2025/8vg0_43196.map" model { file = "/net/cci-nas-00/data/ceres_data/8vg0_43196/01_2025/8vg0_43196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vg0_43196/01_2025/8vg0_43196.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 7.88, per 1000 atoms: 0.60 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: 2.84 Conformation dependent library (CDL) restraints added in 917.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN T 501 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 295 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 292 " pdb="ZN ZN T 501 " - pdb=" SG CYS T 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: 5.55 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: 5.08 Time building geometry restraints manager: 3.40 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: 1.790 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 36.110 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.680 ------------------------------------------------------------------------------- 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 13920 Z= 0.254 Angle : 0.709 10.746 20156 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.001 0.000 TRP T 282 HIS 0.003 0.001 HIS D 82 PHE 0.005 0.001 PHE A 67 TYR 0.028 0.002 TYR D 83 ARG 0.003 0.000 ARG D 79 *********************** 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 : 1.200 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: 0.4243 time to fit residues: 77.6018 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 : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.122013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.072026 restraints weight = 22093.166| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.32 r_work: 0.2750 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13920 Z= 0.236 Angle : 0.583 7.380 20156 Z= 0.354 Chirality : 0.035 0.136 2290 Planarity : 0.004 0.039 1448 Dihedral : 30.177 179.734 4473 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.75 % Allowed : 8.47 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.29), residues: 805 helix: 2.74 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.06 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP T 282 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.037 0.002 TYR D 83 ARG 0.004 0.000 ARG G 11 *********************** 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 140 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8457 (mtp85) cc_final: 0.8232 (mtp85) REVERT: D 101 LEU cc_start: 0.8477 (mt) cc_final: 0.8192 (mt) REVERT: E 59 GLU cc_start: 0.8116 (pm20) cc_final: 0.7851 (pm20) REVERT: F 25 ASN cc_start: 0.8406 (m110) cc_final: 0.8198 (m110) REVERT: H 86 ARG cc_start: 0.8389 (mmt-90) cc_final: 0.7124 (mtm180) outliers start: 12 outliers final: 6 residues processed: 137 average time/residue: 0.3948 time to fit residues: 70.1016 Evaluate side-chains 122 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 80 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 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 F 93 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 = 0.3834 r_free = 0.3834 target = 0.124560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.074816 restraints weight = 22374.960| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.99 r_work: 0.2816 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13920 Z= 0.263 Angle : 0.581 5.502 20156 Z= 0.352 Chirality : 0.035 0.140 2290 Planarity : 0.004 0.035 1448 Dihedral : 30.276 178.020 4473 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.90 % Allowed : 10.95 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.29), residues: 805 helix: 2.74 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.04 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP T 282 HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE A 67 TYR 0.014 0.002 TYR D 40 ARG 0.004 0.000 ARG F 35 *********************** 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 130 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8715 (mtp85) cc_final: 0.8506 (mtp85) REVERT: D 35 GLU cc_start: 0.8523 (pt0) cc_final: 0.8206 (pt0) REVERT: E 59 GLU cc_start: 0.8386 (pm20) cc_final: 0.8023 (pm20) REVERT: H 86 ARG cc_start: 0.8603 (mmt-90) cc_final: 0.7434 (mtm180) REVERT: T 299 MET cc_start: 0.6461 (tmm) cc_final: 0.5659 (pmm) outliers start: 13 outliers final: 11 residues processed: 129 average time/residue: 0.3935 time to fit residues: 66.0593 Evaluate side-chains 125 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 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 99 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 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 = 0.125953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.076231 restraints weight = 22096.788| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.99 r_work: 0.2840 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13920 Z= 0.190 Angle : 0.551 6.144 20156 Z= 0.339 Chirality : 0.033 0.134 2290 Planarity : 0.003 0.034 1448 Dihedral : 30.210 176.786 4473 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.46 % Allowed : 11.53 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.29), residues: 805 helix: 2.86 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.11 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 282 HIS 0.004 0.001 HIS H 49 PHE 0.010 0.001 PHE A 67 TYR 0.015 0.001 TYR D 83 ARG 0.003 0.000 ARG F 35 *********************** 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 135 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8644 (mtp85) cc_final: 0.8150 (mmt90) REVERT: D 35 GLU cc_start: 0.8479 (pt0) cc_final: 0.8141 (pt0) REVERT: D 93 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: E 59 GLU cc_start: 0.8278 (pm20) cc_final: 0.7938 (pm20) REVERT: H 86 ARG cc_start: 0.8576 (mmt-90) cc_final: 0.7430 (mtm180) outliers start: 10 outliers final: 9 residues processed: 133 average time/residue: 0.3981 time to fit residues: 68.2996 Evaluate side-chains 126 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 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 3 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 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 = 0.124337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.075147 restraints weight = 22302.332| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.88 r_work: 0.2838 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13920 Z= 0.239 Angle : 0.569 9.642 20156 Z= 0.344 Chirality : 0.034 0.133 2290 Planarity : 0.003 0.033 1448 Dihedral : 30.391 176.498 4473 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.75 % Allowed : 12.41 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.29), residues: 805 helix: 2.82 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.04 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP T 282 HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.017 0.002 TYR D 83 ARG 0.004 0.000 ARG F 35 *********************** 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 131 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8378 (m-10) cc_final: 0.7890 (m-10) REVERT: D 35 GLU cc_start: 0.8450 (pt0) cc_final: 0.8102 (pt0) REVERT: D 83 TYR cc_start: 0.8325 (m-10) cc_final: 0.7915 (m-10) REVERT: D 93 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: E 59 GLU cc_start: 0.8350 (pm20) cc_final: 0.7978 (pm20) REVERT: E 120 MET cc_start: 0.8396 (mtt) cc_final: 0.8159 (mtt) REVERT: H 68 ASP cc_start: 0.9022 (t0) cc_final: 0.8730 (t0) REVERT: H 86 ARG cc_start: 0.8621 (mmt-90) cc_final: 0.7558 (mtm180) REVERT: T 299 MET cc_start: 0.7111 (tmm) cc_final: 0.6099 (pmm) outliers start: 12 outliers final: 10 residues processed: 131 average time/residue: 0.3846 time to fit residues: 65.8348 Evaluate side-chains 128 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain G residue 114 VAL 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 101 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 125 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 = 0.3857 r_free = 0.3857 target = 0.125748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.076529 restraints weight = 22427.018| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.90 r_work: 0.2858 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13920 Z= 0.187 Angle : 0.551 8.221 20156 Z= 0.336 Chirality : 0.033 0.132 2290 Planarity : 0.003 0.034 1448 Dihedral : 30.229 174.968 4473 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.75 % Allowed : 12.70 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.29), residues: 805 helix: 2.93 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.10 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 282 HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.013 0.001 TYR D 40 ARG 0.004 0.000 ARG F 35 *********************** 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 130 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8426 (m-10) cc_final: 0.8085 (m-10) REVERT: C 13 LYS cc_start: 0.9047 (tptt) cc_final: 0.8716 (tppp) REVERT: D 35 GLU cc_start: 0.8437 (pt0) cc_final: 0.8088 (pt0) REVERT: D 83 TYR cc_start: 0.8397 (m-10) cc_final: 0.8001 (m-10) REVERT: D 93 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: E 59 GLU cc_start: 0.8295 (pm20) cc_final: 0.7932 (pm20) REVERT: E 120 MET cc_start: 0.8317 (mtt) cc_final: 0.8057 (mtt) REVERT: H 86 ARG cc_start: 0.8617 (mmt-90) cc_final: 0.7577 (mtm180) REVERT: T 299 MET cc_start: 0.7090 (tmm) cc_final: 0.6082 (pmm) outliers start: 12 outliers final: 8 residues processed: 127 average time/residue: 0.3865 time to fit residues: 63.8023 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 : 0.985 ------------------------------------------------------------------------------- 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 90 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 19 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 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 = 0.3858 r_free = 0.3858 target = 0.125787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.076527 restraints weight = 22298.557| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.90 r_work: 0.2857 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13920 Z= 0.201 Angle : 0.550 7.587 20156 Z= 0.336 Chirality : 0.033 0.135 2290 Planarity : 0.003 0.034 1448 Dihedral : 30.220 174.564 4473 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.75 % Allowed : 12.85 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.29), residues: 805 helix: 2.97 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.12 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 282 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.015 0.001 TYR D 40 ARG 0.004 0.000 ARG F 35 *********************** 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 130 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8432 (m-10) cc_final: 0.8171 (m-10) REVERT: C 13 LYS cc_start: 0.9024 (tptt) cc_final: 0.8727 (tppp) REVERT: D 35 GLU cc_start: 0.8429 (pt0) cc_final: 0.8075 (pt0) REVERT: D 83 TYR cc_start: 0.8491 (m-10) cc_final: 0.8251 (m-10) REVERT: D 93 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8022 (mp0) REVERT: E 59 GLU cc_start: 0.8269 (pm20) cc_final: 0.7915 (pm20) REVERT: E 120 MET cc_start: 0.8335 (mtt) cc_final: 0.8052 (mtt) REVERT: H 86 ARG cc_start: 0.8621 (mmt-90) cc_final: 0.7582 (mtm180) outliers start: 12 outliers final: 10 residues processed: 128 average time/residue: 0.3986 time to fit residues: 66.3401 Evaluate side-chains 128 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 C residue 36 LYS 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 Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 57 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 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 = 0.3857 r_free = 0.3857 target = 0.125748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.076520 restraints weight = 22357.295| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.90 r_work: 0.2855 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13920 Z= 0.204 Angle : 0.551 7.997 20156 Z= 0.336 Chirality : 0.033 0.135 2290 Planarity : 0.003 0.034 1448 Dihedral : 30.216 173.981 4473 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.61 % Allowed : 12.85 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.29), residues: 805 helix: 2.97 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.14 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP T 282 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.015 0.001 TYR D 40 ARG 0.004 0.000 ARG F 35 *********************** 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 127 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: C 13 LYS cc_start: 0.9023 (tptt) cc_final: 0.8716 (tppp) REVERT: D 35 GLU cc_start: 0.8421 (pt0) cc_final: 0.8068 (pt0) REVERT: D 59 MET cc_start: 0.9001 (tpp) cc_final: 0.8732 (mmm) REVERT: D 93 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: E 59 GLU cc_start: 0.8254 (pm20) cc_final: 0.7906 (pm20) REVERT: E 120 MET cc_start: 0.8341 (mtt) cc_final: 0.8059 (mtt) REVERT: H 86 ARG cc_start: 0.8622 (mmt-90) cc_final: 0.7588 (mtm180) outliers start: 11 outliers final: 10 residues processed: 126 average time/residue: 0.3963 time to fit residues: 65.1896 Evaluate side-chains 127 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 C residue 36 LYS 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 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 55 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 0.0980 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.125835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.076662 restraints weight = 22223.286| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.90 r_work: 0.2866 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13920 Z= 0.198 Angle : 0.551 8.319 20156 Z= 0.336 Chirality : 0.033 0.144 2290 Planarity : 0.003 0.034 1448 Dihedral : 30.204 173.681 4473 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.61 % Allowed : 13.28 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.001 0.000 TRP T 282 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.025 0.002 TYR D 83 ARG 0.004 0.000 ARG F 35 *********************** 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 127 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8417 (m-10) cc_final: 0.7876 (m-10) REVERT: C 13 LYS cc_start: 0.9025 (tptt) cc_final: 0.8729 (tppp) REVERT: D 35 GLU cc_start: 0.8390 (pt0) cc_final: 0.8030 (pt0) REVERT: D 59 MET cc_start: 0.8987 (tpp) cc_final: 0.8709 (mmm) REVERT: D 83 TYR cc_start: 0.8180 (m-10) cc_final: 0.7902 (m-80) REVERT: D 93 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: E 59 GLU cc_start: 0.8234 (pm20) cc_final: 0.7879 (pm20) REVERT: E 120 MET cc_start: 0.8323 (mtt) cc_final: 0.8037 (mtt) REVERT: H 86 ARG cc_start: 0.8612 (mmt-90) cc_final: 0.7581 (mtm180) REVERT: T 299 MET cc_start: 0.7221 (tmm) cc_final: 0.6243 (pmm) outliers start: 11 outliers final: 10 residues processed: 126 average time/residue: 0.3866 time to fit residues: 63.4027 Evaluate side-chains 127 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 C residue 36 LYS 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 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 10 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.124983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.075768 restraints weight = 22203.344| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.91 r_work: 0.2841 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13920 Z= 0.235 Angle : 0.564 8.698 20156 Z= 0.341 Chirality : 0.034 0.144 2290 Planarity : 0.003 0.034 1448 Dihedral : 30.284 173.617 4473 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.75 % Allowed : 13.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.29), residues: 805 helix: 2.90 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.12 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP T 282 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.024 0.002 TYR D 83 ARG 0.005 0.000 ARG F 35 ********************** 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: 12 poor density : 118 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8456 (m-10) cc_final: 0.7897 (m-10) REVERT: C 13 LYS cc_start: 0.9033 (tptt) cc_final: 0.8733 (tppp) REVERT: D 35 GLU cc_start: 0.8397 (pt0) cc_final: 0.8032 (pt0) REVERT: D 83 TYR cc_start: 0.8230 (m-10) cc_final: 0.7928 (m-80) REVERT: D 93 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: E 59 GLU cc_start: 0.8285 (pm20) cc_final: 0.7915 (pm20) REVERT: E 120 MET cc_start: 0.8411 (mtt) cc_final: 0.8151 (mtt) REVERT: H 86 ARG cc_start: 0.8640 (mmt-90) cc_final: 0.7611 (mtm180) REVERT: T 299 MET cc_start: 0.7189 (tmm) cc_final: 0.6223 (pmm) outliers start: 12 outliers final: 8 residues processed: 128 average time/residue: 0.3948 time to fit residues: 65.6574 Evaluate side-chains 125 residues out of total 685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 56 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 37 optimal weight: 0.0270 chunk 13 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.6640 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.124345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.075375 restraints weight = 22433.160| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.09 r_work: 0.2830 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13920 Z= 0.181 Angle : 0.551 8.842 20156 Z= 0.335 Chirality : 0.033 0.138 2290 Planarity : 0.003 0.034 1448 Dihedral : 30.213 173.069 4473 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.29), residues: 805 helix: 2.94 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.15 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP T 282 HIS 0.002 0.000 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.021 0.001 TYR D 83 ARG 0.005 0.000 ARG F 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6025.03 seconds wall clock time: 108 minutes 7.69 seconds (6487.69 seconds total)