Starting phenix.real_space_refine on Sat Oct 12 16:15:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vg0_43196/10_2024/8vg0_43196.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vg0_43196/10_2024/8vg0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vg0_43196/10_2024/8vg0_43196.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vg0_43196/10_2024/8vg0_43196.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vg0_43196/10_2024/8vg0_43196.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vg0_43196/10_2024/8vg0_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 7.96, per 1000 atoms: 0.61 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: 3.23 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 6.77 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: 5.70 Time building geometry restraints manager: 3.80 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: 1.670 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 39.440 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.090 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.053 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: 0.4294 time to fit residues: 78.5586 Evaluate side-chains 123 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8193 (pm20) cc_final: 0.7947 (pm20) REVERT: A 76 GLN cc_start: 0.8539 (tp40) cc_final: 0.8333 (tp40) REVERT: B 95 ARG cc_start: 0.8416 (mtp85) cc_final: 0.8179 (mtp85) REVERT: D 101 LEU cc_start: 0.8455 (mt) cc_final: 0.8179 (mt) REVERT: E 59 GLU cc_start: 0.8115 (pm20) cc_final: 0.7834 (pm20) REVERT: F 25 ASN cc_start: 0.8383 (m110) cc_final: 0.8164 (m110) REVERT: H 86 ARG cc_start: 0.8350 (mmt-90) cc_final: 0.7081 (mtm180) outliers start: 12 outliers final: 6 residues processed: 137 average time/residue: 0.3963 time to fit residues: 70.0557 Evaluate side-chains 122 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 0.0770 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1215 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= 0.183 Angle : 0.558 5.798 20156 Z= 0.342 Chirality : 0.034 0.141 2290 Planarity : 0.004 0.034 1448 Dihedral : 30.088 177.347 4473 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.46 % Allowed : 11.09 % Favored : 87.45 % 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: 3.12 (0.29), residues: 805 helix: 2.86 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.16 (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 F 75 PHE 0.010 0.001 PHE A 67 TYR 0.015 0.001 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 132 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: C 74 LYS cc_start: 0.8890 (mtpp) cc_final: 0.8593 (mtpp) REVERT: D 35 GLU cc_start: 0.8581 (pt0) cc_final: 0.8255 (pt0) REVERT: D 93 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: E 59 GLU cc_start: 0.8069 (pm20) cc_final: 0.7471 (pm20) REVERT: F 25 ASN cc_start: 0.8406 (m110) cc_final: 0.8098 (m110) REVERT: H 86 ARG cc_start: 0.8300 (mmt-90) cc_final: 0.7077 (mtm180) REVERT: T 299 MET cc_start: 0.6437 (tmm) cc_final: 0.5641 (pmm) outliers start: 10 outliers final: 8 residues processed: 129 average time/residue: 0.3924 time to fit residues: 65.4593 Evaluate side-chains 125 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 47 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 0.0030 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 0.0870 chunk 28 optimal weight: 5.9990 overall best weight: 0.4368 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13920 Z= 0.166 Angle : 0.544 6.409 20156 Z= 0.335 Chirality : 0.033 0.136 2290 Planarity : 0.003 0.036 1448 Dihedral : 30.060 175.907 4473 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.02 % Allowed : 12.26 % Favored : 86.72 % 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: 3.27 (0.29), residues: 805 helix: 2.96 (0.21), residues: 561 sheet: None (None), residues: 0 loop : 0.24 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 282 HIS 0.002 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.036 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 128 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.7939 (m-10) cc_final: 0.7591 (m-10) REVERT: D 35 GLU cc_start: 0.8559 (pt0) cc_final: 0.8211 (pt0) REVERT: D 83 TYR cc_start: 0.8071 (m-10) cc_final: 0.7731 (m-80) REVERT: D 93 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8001 (mp0) REVERT: E 59 GLU cc_start: 0.7743 (pm20) cc_final: 0.7381 (pm20) REVERT: F 25 ASN cc_start: 0.8396 (m110) cc_final: 0.8044 (m110) REVERT: F 95 ARG cc_start: 0.8097 (mtp85) cc_final: 0.7729 (ttm-80) REVERT: H 86 ARG cc_start: 0.8281 (mmt-90) cc_final: 0.7050 (mtm180) outliers start: 7 outliers final: 5 residues processed: 126 average time/residue: 0.4055 time to fit residues: 65.6400 Evaluate side-chains 123 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1710 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 : 0.553 8.794 20156 Z= 0.336 Chirality : 0.033 0.133 2290 Planarity : 0.003 0.033 1448 Dihedral : 30.220 175.451 4473 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.61 % Allowed : 12.99 % 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: 3.27 (0.29), residues: 805 helix: 2.99 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.17 (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 F 75 PHE 0.008 0.001 PHE A 67 TYR 0.032 0.002 TYR D 83 ARG 0.003 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 134 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: D 35 GLU cc_start: 0.8559 (pt0) cc_final: 0.8207 (pt0) REVERT: E 59 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7322 (pm20) REVERT: F 25 ASN cc_start: 0.8437 (m110) cc_final: 0.8091 (m110) REVERT: F 95 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7792 (ttm-80) REVERT: H 86 ARG cc_start: 0.8288 (mmt-90) cc_final: 0.7095 (mtm180) REVERT: T 299 MET cc_start: 0.7087 (tmm) cc_final: 0.6043 (pmm) outliers start: 11 outliers final: 6 residues processed: 130 average time/residue: 0.4021 time to fit residues: 67.5093 Evaluate side-chains 130 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 19 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1820 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= 0.208 Angle : 0.551 8.305 20156 Z= 0.336 Chirality : 0.033 0.139 2290 Planarity : 0.003 0.034 1448 Dihedral : 30.174 174.416 4473 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.90 % Allowed : 12.55 % 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: 3.27 (0.29), residues: 805 helix: 3.00 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.15 (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 F 75 PHE 0.008 0.001 PHE A 67 TYR 0.025 0.002 TYR D 83 ARG 0.005 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 133 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: C 13 LYS cc_start: 0.9021 (tptt) cc_final: 0.8705 (tppp) REVERT: D 35 GLU cc_start: 0.8548 (pt0) cc_final: 0.8185 (pt0) REVERT: D 93 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: E 59 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7332 (pm20) REVERT: F 25 ASN cc_start: 0.8467 (m110) cc_final: 0.8103 (m110) REVERT: H 86 ARG cc_start: 0.8294 (mmt-90) cc_final: 0.7106 (mtm180) REVERT: T 299 MET cc_start: 0.7156 (tmm) cc_final: 0.6173 (pmm) outliers start: 13 outliers final: 9 residues processed: 129 average time/residue: 0.4071 time to fit residues: 67.9331 Evaluate side-chains 129 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 115 LYS 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 E residue 59 GLU Chi-restraints excluded: chain F residue 50 ILE 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 100 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 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: H 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1869 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 7.607 20156 Z= 0.335 Chirality : 0.033 0.164 2290 Planarity : 0.003 0.034 1448 Dihedral : 30.149 173.749 4473 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.61 % Allowed : 13.14 % 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 (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: 3.29 (0.29), residues: 805 helix: 3.02 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.16 (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 0.009 0.001 PHE A 67 TYR 0.053 0.002 TYR D 83 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 129 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.7893 (mmm) cc_final: 0.7575 (mmm) REVERT: C 13 LYS cc_start: 0.9028 (tptt) cc_final: 0.8710 (tppp) REVERT: D 35 GLU cc_start: 0.8515 (pt0) cc_final: 0.8148 (pt0) REVERT: D 59 MET cc_start: 0.8774 (tpp) cc_final: 0.8499 (mmm) REVERT: D 93 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7957 (mp0) REVERT: E 59 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7309 (pm20) REVERT: F 25 ASN cc_start: 0.8474 (m110) cc_final: 0.8084 (m110) REVERT: H 86 ARG cc_start: 0.8290 (mmt-90) cc_final: 0.7108 (mtm180) REVERT: T 299 MET cc_start: 0.7156 (tmm) cc_final: 0.6183 (pmm) outliers start: 11 outliers final: 9 residues processed: 126 average time/residue: 0.3809 time to fit residues: 62.5329 Evaluate side-chains 129 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 115 LYS 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 E residue 59 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 19 SER 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 41 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13920 Z= 0.243 Angle : 0.564 7.213 20156 Z= 0.342 Chirality : 0.034 0.174 2290 Planarity : 0.004 0.033 1448 Dihedral : 30.294 173.784 4473 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.61 % Allowed : 12.99 % 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: 3.20 (0.29), residues: 805 helix: 2.94 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.13 (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 F 75 PHE 0.008 0.001 PHE A 67 TYR 0.022 0.002 TYR D 83 ARG 0.005 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 131 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.7874 (m-10) cc_final: 0.7654 (m-10) REVERT: C 13 LYS cc_start: 0.9023 (tptt) cc_final: 0.8720 (tppp) REVERT: D 35 GLU cc_start: 0.8518 (pt0) cc_final: 0.8143 (pt0) REVERT: D 83 TYR cc_start: 0.7827 (m-10) cc_final: 0.7557 (m-80) REVERT: D 93 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: E 59 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7302 (pm20) REVERT: F 25 ASN cc_start: 0.8494 (m110) cc_final: 0.8152 (m110) REVERT: H 86 ARG cc_start: 0.8308 (mmt-90) cc_final: 0.7186 (mtm180) REVERT: T 299 MET cc_start: 0.7155 (tmm) cc_final: 0.6186 (pmm) outliers start: 11 outliers final: 8 residues processed: 129 average time/residue: 0.3891 time to fit residues: 64.9844 Evaluate side-chains 129 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 E residue 59 GLU 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 90 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2013 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= 0.193 Angle : 0.554 8.640 20156 Z= 0.336 Chirality : 0.033 0.166 2290 Planarity : 0.003 0.034 1448 Dihedral : 30.185 173.004 4473 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: 3.26 (0.29), residues: 805 helix: 2.99 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.16 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP T 282 HIS 0.003 0.000 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.018 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 128 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.7863 (m-10) cc_final: 0.7604 (m-10) REVERT: C 13 LYS cc_start: 0.9019 (tptt) cc_final: 0.8725 (tppp) REVERT: D 35 GLU cc_start: 0.8496 (pt0) cc_final: 0.8120 (pt0) REVERT: D 59 MET cc_start: 0.8779 (tpp) cc_final: 0.8534 (mmm) REVERT: D 83 TYR cc_start: 0.7830 (m-10) cc_final: 0.7533 (m-80) REVERT: D 93 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: E 59 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7226 (pm20) REVERT: F 25 ASN cc_start: 0.8491 (m110) cc_final: 0.8131 (m110) REVERT: H 86 ARG cc_start: 0.8294 (mmt-90) cc_final: 0.7184 (mtm180) REVERT: T 299 MET cc_start: 0.7153 (tmm) cc_final: 0.6186 (pmm) outliers start: 11 outliers final: 9 residues processed: 125 average time/residue: 0.3835 time to fit residues: 62.2829 Evaluate side-chains 128 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 59 GLU 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 102 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13920 Z= 0.210 Angle : 0.560 9.013 20156 Z= 0.338 Chirality : 0.033 0.170 2290 Planarity : 0.003 0.034 1448 Dihedral : 30.192 172.829 4473 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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 (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: 2.94 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.16 (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 F 75 PHE 0.009 0.001 PHE A 67 TYR 0.017 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 127 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: C 13 LYS cc_start: 0.9022 (tptt) cc_final: 0.8726 (tppp) REVERT: D 35 GLU cc_start: 0.8497 (pt0) cc_final: 0.8117 (pt0) REVERT: D 59 MET cc_start: 0.8788 (tpp) cc_final: 0.8533 (mmm) REVERT: D 83 TYR cc_start: 0.7835 (m-10) cc_final: 0.7526 (m-80) REVERT: D 93 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: E 59 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7227 (pm20) REVERT: F 25 ASN cc_start: 0.8491 (m110) cc_final: 0.8141 (m110) REVERT: H 86 ARG cc_start: 0.8303 (mmt-90) cc_final: 0.7193 (mtm180) REVERT: T 299 MET cc_start: 0.7144 (tmm) cc_final: 0.6176 (pmm) outliers start: 10 outliers final: 8 residues processed: 125 average time/residue: 0.3851 time to fit residues: 62.4211 Evaluate side-chains 127 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 E residue 59 GLU 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 91 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.124265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.075092 restraints weight = 22178.802| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.91 r_work: 0.2836 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2088 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= 0.264 Angle : 0.577 9.229 20156 Z= 0.347 Chirality : 0.034 0.172 2290 Planarity : 0.004 0.034 1448 Dihedral : 30.376 173.359 4473 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.61 % Allowed : 13.43 % 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: 3.11 (0.29), residues: 805 helix: 2.87 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 0.12 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP T 282 HIS 0.003 0.001 HIS B 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2445.18 seconds wall clock time: 45 minutes 18.30 seconds (2718.30 seconds total)