Starting phenix.real_space_refine on Sun Mar 17 13:55:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/03_2024/8c9a_16507.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/03_2024/8c9a_16507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/03_2024/8c9a_16507.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/03_2024/8c9a_16507.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/03_2024/8c9a_16507.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/03_2024/8c9a_16507.pdb" } resolution = 4.86 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= 0.000 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 650 5.49 5 S 10 5.16 5 C 8805 2.51 5 N 3358 2.21 5 O 5236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18059 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 13953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 13953 Classifications: {'RNA': 650} Modifications used: {'rna2p_pur': 70, 'rna2p_pyr': 42, 'rna3p_pur': 314, 'rna3p_pyr': 224} Link IDs: {'rna2p': 112, 'rna3p': 537} Chain breaks: 5 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {' U%rna2p_pyr:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "2" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 286 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1137 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain breaks: 1 Chain: "S" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 726 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 1 Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "Y" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 494 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "T" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 684 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain breaks: 1 Time building chain proxies: 9.82, per 1000 atoms: 0.54 Number of scatterers: 18059 At special positions: 0 Unit cell: (132.5, 152.5, 148.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 650 15.00 O 5236 8.00 N 3358 7.00 C 8805 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 - 3.50 Amino acid : False - 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: 10.52 Conformation dependent library (CDL) restraints added in 924.0 milliseconds 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 998 Finding SS restraints... Warning! N1 atom is missing from residue G A 356 Was trying to link: G A 356 N1 with U A 284 O4, Saenger class: 27 Warning! N1 atom is missing from residue G A 356 Was trying to link: G A 356 N1 with U A 284 O2, Saenger class: 28 Secondary structure from input PDB file: 19 helices and 5 sheets defined 44.6% alpha, 14.7% beta 198 base pairs and 310 stacking pairs defined. Time for finding SS restraints: 8.72 Creating SS restraints... Processing helix chain '2' and resid 10 through 17 Processing helix chain '2' and resid 17 through 24 removed outlier: 4.282A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 38 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.689A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.566A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 201 Processing helix chain 'S' and resid 13 through 22 Processing helix chain 'S' and resid 28 through 38 removed outlier: 4.349A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 63 removed outlier: 3.789A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 67 No H-bonds generated for 'chain 'U' and resid 65 through 67' Processing helix chain 'Y' and resid 9 through 35 removed outlier: 3.525A pdb=" N GLU Y 13 " --> pdb=" O LYS Y 9 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 56 removed outlier: 3.817A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU Y 56 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 9 removed outlier: 3.531A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 removed outlier: 3.847A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 52 Processing sheet with id=AA1, first strand: chain 'E' and resid 118 through 121 removed outlier: 4.005A pdb=" N THR E 189 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 3 through 10 removed outlier: 5.340A pdb=" N ILE S 4 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL S 107 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LYS S 6 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL S 105 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ARG S 8 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE S 103 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'U' and resid 33 through 35 removed outlier: 7.123A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP U 8 " --> pdb=" O VAL U 24 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'U' and resid 83 through 86 Processing sheet with id=AA5, first strand: chain 'T' and resid 29 through 34 removed outlier: 3.604A pdb=" N ALA T 83 " --> pdb=" O LEU T 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL T 34 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR T 86 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) 181 hydrogen bonds defined for protein. 534 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 506 hydrogen bonds 816 hydrogen bond angles 0 basepair planarities 198 basepair parallelities 310 stacking parallelities Total time for adding SS restraints: 8.96 Time building geometry restraints manager: 11.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2914 1.33 - 1.45: 8282 1.45 - 1.57: 7252 1.57 - 1.69: 1294 1.69 - 1.81: 20 Bond restraints: 19762 Sorted by residual: bond pdb=" N ALA U 1 " pdb=" CA ALA U 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N MET Y 1 " pdb=" CA MET Y 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N MET T 1 " pdb=" CA MET T 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.84e+00 bond pdb=" C5 G A 356 " pdb=" C4 G A 356 " ideal model delta sigma weight residual 1.379 1.397 -0.018 2.00e-02 2.50e+03 8.39e-01 bond pdb=" C5 A A 278 " pdb=" C6 A A 278 " ideal model delta sigma weight residual 1.406 1.422 -0.016 2.00e-02 2.50e+03 6.21e-01 ... (remaining 19757 not shown) Histogram of bond angle deviations from ideal: 81.29 - 91.90: 2 91.90 - 102.51: 800 102.51 - 113.12: 14581 113.12 - 123.74: 11494 123.74 - 134.35: 3017 Bond angle restraints: 29894 Sorted by residual: angle pdb=" O3' C A 624 " pdb=" P G A 625 " pdb=" OP1 G A 625 " ideal model delta sigma weight residual 108.00 81.29 26.71 3.00e+00 1.11e-01 7.93e+01 angle pdb=" O3' C A 624 " pdb=" P G A 625 " pdb=" OP2 G A 625 " ideal model delta sigma weight residual 108.00 84.09 23.91 3.00e+00 1.11e-01 6.35e+01 angle pdb=" O3' C A 624 " pdb=" P G A 625 " pdb=" O5' G A 625 " ideal model delta sigma weight residual 104.00 98.81 5.19 1.50e+00 4.44e-01 1.20e+01 angle pdb=" OP1 G A 625 " pdb=" P G A 625 " pdb=" OP2 G A 625 " ideal model delta sigma weight residual 119.60 129.76 -10.16 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C6 A A 278 " pdb=" N1 A A 278 " pdb=" C2 A A 278 " ideal model delta sigma weight residual 118.60 127.77 -9.17 3.00e+00 1.11e-01 9.34e+00 ... (remaining 29889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 11083 35.82 - 71.63: 1350 71.63 - 107.45: 182 107.45 - 143.27: 2 143.27 - 179.09: 3 Dihedral angle restraints: 12620 sinusoidal: 11102 harmonic: 1518 Sorted by residual: dihedral pdb=" O4' C A 140 " pdb=" C1' C A 140 " pdb=" N1 C A 140 " pdb=" C2 C A 140 " ideal model delta sinusoidal sigma weight residual -128.00 35.65 -163.65 1 1.70e+01 3.46e-03 6.51e+01 dihedral pdb=" O4' U A1313 " pdb=" C1' U A1313 " pdb=" N1 U A1313 " pdb=" C2 U A1313 " ideal model delta sinusoidal sigma weight residual 200.00 108.07 91.93 1 1.50e+01 4.44e-03 4.41e+01 dihedral pdb=" O4' A A 632 " pdb=" C1' A A 632 " pdb=" N9 A A 632 " pdb=" C4 A A 632 " ideal model delta sinusoidal sigma weight residual 68.00 128.32 -60.32 1 1.70e+01 3.46e-03 1.68e+01 ... (remaining 12617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.400: 3912 0.400 - 0.801: 0 0.801 - 1.201: 0 1.201 - 1.602: 0 1.602 - 2.002: 1 Chirality restraints: 3913 Sorted by residual: chirality pdb=" P G A 625 " pdb=" OP1 G A 625 " pdb=" OP2 G A 625 " pdb=" O5' G A 625 " both_signs ideal model delta sigma weight residual True 2.41 0.41 2.00 2.00e-01 2.50e+01 1.00e+02 chirality pdb=" CA ILE E 148 " pdb=" N ILE E 148 " pdb=" C ILE E 148 " pdb=" CB ILE E 148 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" C3' U A 148 " pdb=" C4' U A 148 " pdb=" O3' U A 148 " pdb=" C2' U A 148 " both_signs ideal model delta sigma weight residual False -2.74 -2.60 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 3910 not shown) Planarity restraints: 1349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 33 " 0.009 2.00e-02 2.50e+03 1.24e-02 3.47e+00 pdb=" N1 C A 33 " -0.002 2.00e-02 2.50e+03 pdb=" C2 C A 33 " 0.025 2.00e-02 2.50e+03 pdb=" O2 C A 33 " -0.022 2.00e-02 2.50e+03 pdb=" N3 C A 33 " -0.001 2.00e-02 2.50e+03 pdb=" C4 C A 33 " 0.005 2.00e-02 2.50e+03 pdb=" N4 C A 33 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C A 33 " -0.009 2.00e-02 2.50e+03 pdb=" C6 C A 33 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 363 " -0.007 2.00e-02 2.50e+03 1.00e-02 3.01e+00 pdb=" N9 G A 363 " 0.004 2.00e-02 2.50e+03 pdb=" C8 G A 363 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G A 363 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G A 363 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G A 363 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G A 363 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G A 363 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G A 363 " 0.027 2.00e-02 2.50e+03 pdb=" N2 G A 363 " -0.019 2.00e-02 2.50e+03 pdb=" N3 G A 363 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G A 363 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 473 " 0.006 2.00e-02 2.50e+03 9.37e-03 2.63e+00 pdb=" N9 G A 473 " -0.002 2.00e-02 2.50e+03 pdb=" C8 G A 473 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G A 473 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G A 473 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G A 473 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G A 473 " 0.007 2.00e-02 2.50e+03 pdb=" N1 G A 473 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G A 473 " -0.025 2.00e-02 2.50e+03 pdb=" N2 G A 473 " 0.017 2.00e-02 2.50e+03 pdb=" N3 G A 473 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G A 473 " 0.000 2.00e-02 2.50e+03 ... (remaining 1346 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 160 2.52 - 3.11: 13075 3.11 - 3.71: 33605 3.71 - 4.30: 45916 4.30 - 4.90: 62873 Nonbonded interactions: 155629 Sorted by model distance: nonbonded pdb=" O2' A A 255 " pdb=" O4' A A 256 " model vdw 1.924 2.440 nonbonded pdb=" O2 C A 69 " pdb=" O2' A A 73 " model vdw 1.948 2.440 nonbonded pdb=" O2 C A 106 " pdb=" O2' A A 294 " model vdw 1.965 2.440 nonbonded pdb=" O2' A A 126 " pdb=" O4' A A 127 " model vdw 1.975 2.440 nonbonded pdb=" O2' A A 299 " pdb=" O4' A A 300 " model vdw 1.988 2.440 ... (remaining 155624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 6.370 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 58.160 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 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 : 0.001 0.033 19762 Z= 0.082 Angle : 0.451 26.711 29894 Z= 0.212 Chirality : 0.040 2.002 3913 Planarity : 0.002 0.022 1349 Dihedral : 22.913 179.086 11622 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.23 % Allowed : 3.39 % Favored : 96.39 % 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: 1.73 (0.39), residues: 507 helix: 2.53 (0.37), residues: 213 sheet: 0.56 (0.67), residues: 71 loop : 0.03 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP T 80 HIS 0.001 0.000 HIS S 102 PHE 0.005 0.001 PHE S 75 TYR 0.005 0.001 TYR T 84 ARG 0.002 0.000 ARG 2 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8920 (tm-30) REVERT: E 149 ILE cc_start: 0.9481 (tp) cc_final: 0.8987 (tp) REVERT: E 188 MET cc_start: 0.8631 (ttt) cc_final: 0.8222 (tpt) REVERT: E 195 GLN cc_start: 0.9690 (mt0) cc_final: 0.9289 (mt0) REVERT: E 199 MET cc_start: 0.8842 (mtm) cc_final: 0.8132 (ptp) REVERT: S 68 ASP cc_start: 0.9274 (t0) cc_final: 0.8858 (t70) REVERT: U 12 VAL cc_start: 0.8571 (t) cc_final: 0.8029 (t) REVERT: T 1 MET cc_start: 0.6162 (pmm) cc_final: 0.5517 (pmm) REVERT: T 80 TRP cc_start: 0.6633 (p-90) cc_final: 0.6382 (t60) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.3568 time to fit residues: 52.8284 Evaluate side-chains 63 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 58 optimal weight: 30.0000 chunk 46 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 104 optimal weight: 0.1980 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN T 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 19762 Z= 0.354 Angle : 0.853 28.380 29894 Z= 0.409 Chirality : 0.050 1.915 3913 Planarity : 0.005 0.050 1349 Dihedral : 24.623 172.281 10573 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 31.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.23 % Allowed : 5.87 % Favored : 93.91 % 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: 0.02 (0.36), residues: 507 helix: 0.61 (0.33), residues: 219 sheet: 0.35 (0.57), residues: 79 loop : -0.66 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP T 80 HIS 0.007 0.002 HIS S 60 PHE 0.019 0.002 PHE Y 26 TYR 0.020 0.002 TYR T 84 ARG 0.005 0.001 ARG Y 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 188 MET cc_start: 0.8847 (ttt) cc_final: 0.8497 (tpt) REVERT: E 195 GLN cc_start: 0.9672 (mt0) cc_final: 0.9340 (mt0) REVERT: E 199 MET cc_start: 0.9132 (mtm) cc_final: 0.8445 (ptp) REVERT: Y 27 ASN cc_start: 0.9524 (m110) cc_final: 0.9307 (p0) REVERT: T 51 PHE cc_start: 0.8813 (m-80) cc_final: 0.8495 (m-80) REVERT: T 80 TRP cc_start: 0.7223 (p-90) cc_final: 0.6957 (t60) outliers start: 1 outliers final: 1 residues processed: 82 average time/residue: 0.3417 time to fit residues: 41.1283 Evaluate side-chains 56 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 30.0000 chunk 32 optimal weight: 7.9990 chunk 86 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19762 Z= 0.268 Angle : 0.712 26.956 29894 Z= 0.343 Chirality : 0.046 1.952 3913 Planarity : 0.005 0.037 1349 Dihedral : 24.993 174.399 10573 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 29.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % 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: -0.49 (0.36), residues: 507 helix: 0.27 (0.32), residues: 218 sheet: -0.71 (0.51), residues: 96 loop : -0.60 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP T 80 HIS 0.004 0.001 HIS Y 41 PHE 0.015 0.002 PHE Y 26 TYR 0.014 0.002 TYR T 84 ARG 0.005 0.001 ARG 2 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 102 ARG cc_start: 0.9308 (ptt180) cc_final: 0.9038 (mtm-85) REVERT: E 149 ILE cc_start: 0.9483 (tp) cc_final: 0.9192 (tp) REVERT: E 188 MET cc_start: 0.8768 (ttt) cc_final: 0.8499 (tpt) REVERT: E 195 GLN cc_start: 0.9727 (mt0) cc_final: 0.9254 (mt0) REVERT: E 199 MET cc_start: 0.9197 (mtm) cc_final: 0.8380 (ptp) REVERT: S 68 ASP cc_start: 0.9493 (t0) cc_final: 0.9271 (t70) REVERT: U 7 ASP cc_start: 0.8488 (m-30) cc_final: 0.8263 (m-30) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.3641 time to fit residues: 41.1674 Evaluate side-chains 57 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 92 optimal weight: 0.5980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN S 61 ASN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.6146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19762 Z= 0.226 Angle : 0.662 27.259 29894 Z= 0.317 Chirality : 0.045 1.936 3913 Planarity : 0.004 0.031 1349 Dihedral : 24.940 172.840 10573 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 27.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.23 % Allowed : 2.71 % Favored : 97.07 % 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: -0.49 (0.35), residues: 507 helix: 0.46 (0.33), residues: 218 sheet: -0.88 (0.49), residues: 94 loop : -0.79 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP T 80 HIS 0.003 0.001 HIS Y 41 PHE 0.015 0.002 PHE Y 26 TYR 0.013 0.002 TYR T 84 ARG 0.007 0.001 ARG U 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 102 ARG cc_start: 0.9268 (ptt180) cc_final: 0.8932 (ptt-90) REVERT: E 117 ARG cc_start: 0.6375 (mtp180) cc_final: 0.6088 (mtp180) REVERT: E 195 GLN cc_start: 0.9723 (mt0) cc_final: 0.9226 (mt0) REVERT: E 199 MET cc_start: 0.9314 (mtm) cc_final: 0.8585 (mtp) REVERT: U 7 ASP cc_start: 0.8497 (m-30) cc_final: 0.8281 (m-30) REVERT: T 32 LEU cc_start: 0.8692 (mt) cc_final: 0.8415 (mp) REVERT: T 51 PHE cc_start: 0.8848 (m-80) cc_final: 0.8456 (m-80) outliers start: 1 outliers final: 1 residues processed: 77 average time/residue: 0.3589 time to fit residues: 39.8780 Evaluate side-chains 57 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.7888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 19762 Z= 0.398 Angle : 0.891 27.579 29894 Z= 0.429 Chirality : 0.053 1.920 3913 Planarity : 0.006 0.054 1349 Dihedral : 25.806 170.279 10573 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 46.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % 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: -1.53 (0.33), residues: 507 helix: -0.26 (0.31), residues: 219 sheet: -1.72 (0.46), residues: 98 loop : -1.31 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP T 80 HIS 0.006 0.002 HIS Y 41 PHE 0.021 0.003 PHE U 94 TYR 0.014 0.003 TYR T 84 ARG 0.009 0.001 ARG Y 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 GLU cc_start: 0.9221 (pp20) cc_final: 0.8896 (pm20) REVERT: E 117 ARG cc_start: 0.6372 (mtp180) cc_final: 0.6151 (mtp180) REVERT: E 199 MET cc_start: 0.9356 (mtm) cc_final: 0.8638 (mtp) REVERT: T 32 LEU cc_start: 0.8751 (mt) cc_final: 0.8539 (mp) REVERT: T 51 PHE cc_start: 0.8852 (m-80) cc_final: 0.8527 (m-80) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.3764 time to fit residues: 38.1256 Evaluate side-chains 49 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 58 optimal weight: 30.0000 chunk 107 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.7936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 19762 Z= 0.290 Angle : 0.742 27.198 29894 Z= 0.357 Chirality : 0.048 1.935 3913 Planarity : 0.005 0.032 1349 Dihedral : 25.571 166.083 10573 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 35.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.23 % Allowed : 3.16 % Favored : 96.61 % 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: -1.22 (0.34), residues: 507 helix: 0.12 (0.33), residues: 219 sheet: -1.23 (0.47), residues: 87 loop : -1.56 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP T 80 HIS 0.003 0.001 HIS Y 41 PHE 0.017 0.002 PHE Y 26 TYR 0.012 0.002 TYR T 84 ARG 0.006 0.001 ARG Y 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 GLU cc_start: 0.9190 (pp20) cc_final: 0.8888 (pm20) REVERT: E 117 ARG cc_start: 0.6297 (mtp180) cc_final: 0.5496 (mtp180) REVERT: E 199 MET cc_start: 0.9479 (mtm) cc_final: 0.8863 (mtm) REVERT: T 11 LEU cc_start: 0.8882 (pt) cc_final: 0.8588 (pp) REVERT: T 32 LEU cc_start: 0.8612 (mt) cc_final: 0.8340 (mp) REVERT: T 51 PHE cc_start: 0.8858 (m-80) cc_final: 0.8555 (m-80) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.3597 time to fit residues: 39.2319 Evaluate side-chains 48 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 81 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.7865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 19762 Z= 0.213 Angle : 0.668 27.115 29894 Z= 0.321 Chirality : 0.045 1.939 3913 Planarity : 0.004 0.049 1349 Dihedral : 25.320 167.432 10573 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 27.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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: -1.15 (0.34), residues: 507 helix: 0.15 (0.33), residues: 223 sheet: -1.37 (0.48), residues: 88 loop : -1.42 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 80 HIS 0.003 0.001 HIS Y 41 PHE 0.014 0.002 PHE E 124 TYR 0.011 0.002 TYR T 84 ARG 0.009 0.001 ARG E 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 GLU cc_start: 0.9165 (pp20) cc_final: 0.8873 (pm20) REVERT: E 100 MET cc_start: 0.9235 (mtt) cc_final: 0.8786 (mtp) REVERT: E 117 ARG cc_start: 0.6351 (mtp180) cc_final: 0.6075 (mtp180) REVERT: E 199 MET cc_start: 0.9342 (mtm) cc_final: 0.8494 (ptm) REVERT: Y 1 MET cc_start: 0.8417 (tpt) cc_final: 0.8063 (tpp) REVERT: Y 4 LYS cc_start: 0.9424 (pptt) cc_final: 0.9171 (pptt) REVERT: T 11 LEU cc_start: 0.8858 (pt) cc_final: 0.8560 (pp) REVERT: T 32 LEU cc_start: 0.8557 (mt) cc_final: 0.8286 (mp) REVERT: T 51 PHE cc_start: 0.8744 (m-80) cc_final: 0.8419 (m-80) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.3734 time to fit residues: 37.8872 Evaluate side-chains 50 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.8155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19762 Z= 0.238 Angle : 0.692 27.233 29894 Z= 0.332 Chirality : 0.046 1.935 3913 Planarity : 0.005 0.049 1349 Dihedral : 25.383 169.189 10573 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 31.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.19 (0.34), residues: 507 helix: 0.19 (0.33), residues: 223 sheet: -1.33 (0.48), residues: 84 loop : -1.57 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 80 HIS 0.003 0.001 HIS Y 41 PHE 0.014 0.002 PHE Y 26 TYR 0.012 0.002 TYR T 84 ARG 0.005 0.001 ARG Y 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 GLU cc_start: 0.9164 (pp20) cc_final: 0.8881 (pm20) REVERT: E 100 MET cc_start: 0.9090 (mtt) cc_final: 0.8645 (mtp) REVERT: E 184 ASP cc_start: 0.9116 (t70) cc_final: 0.8892 (t0) REVERT: E 199 MET cc_start: 0.9238 (mtm) cc_final: 0.8516 (ptm) REVERT: U 7 ASP cc_start: 0.8659 (m-30) cc_final: 0.8458 (m-30) REVERT: Y 1 MET cc_start: 0.8484 (tpt) cc_final: 0.7966 (tpp) REVERT: Y 7 ARG cc_start: 0.9178 (ptp-110) cc_final: 0.8527 (ttp80) REVERT: T 11 LEU cc_start: 0.8917 (pt) cc_final: 0.8651 (pp) REVERT: T 29 THR cc_start: 0.7941 (m) cc_final: 0.7685 (m) REVERT: T 32 LEU cc_start: 0.8417 (mt) cc_final: 0.8186 (mp) REVERT: T 51 PHE cc_start: 0.8788 (m-80) cc_final: 0.8519 (m-80) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.3715 time to fit residues: 38.4709 Evaluate side-chains 48 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 62 optimal weight: 30.0000 chunk 44 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.8616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19762 Z= 0.258 Angle : 0.719 27.192 29894 Z= 0.347 Chirality : 0.047 1.934 3913 Planarity : 0.005 0.052 1349 Dihedral : 25.479 166.758 10573 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 33.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.23 % Allowed : 1.35 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.46 (0.35), residues: 507 helix: -0.11 (0.33), residues: 222 sheet: -1.57 (0.47), residues: 87 loop : -1.55 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 80 HIS 0.003 0.001 HIS Y 41 PHE 0.013 0.002 PHE Y 26 TYR 0.009 0.002 TYR T 84 ARG 0.005 0.001 ARG Y 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 25 GLU cc_start: 0.9194 (pp20) cc_final: 0.8921 (pm20) REVERT: E 100 MET cc_start: 0.9164 (mtt) cc_final: 0.8759 (mtp) REVERT: E 199 MET cc_start: 0.9239 (mtm) cc_final: 0.8588 (mtm) REVERT: Y 1 MET cc_start: 0.8547 (tpt) cc_final: 0.8097 (tpp) REVERT: Y 7 ARG cc_start: 0.9153 (ptp-110) cc_final: 0.8561 (ttp80) REVERT: T 11 LEU cc_start: 0.8863 (pt) cc_final: 0.8617 (pp) REVERT: T 29 THR cc_start: 0.7892 (m) cc_final: 0.7602 (m) REVERT: T 31 VAL cc_start: 0.8759 (t) cc_final: 0.8555 (t) REVERT: T 32 LEU cc_start: 0.8503 (mt) cc_final: 0.8203 (mp) REVERT: T 51 PHE cc_start: 0.8806 (m-80) cc_final: 0.8442 (m-80) outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.3720 time to fit residues: 36.6805 Evaluate side-chains 45 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 72 optimal weight: 0.1980 chunk 97 optimal weight: 8.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.8735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19762 Z= 0.248 Angle : 0.706 27.222 29894 Z= 0.340 Chirality : 0.046 1.936 3913 Planarity : 0.005 0.034 1349 Dihedral : 25.459 167.499 10573 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 32.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -1.52 (0.34), residues: 507 helix: -0.15 (0.33), residues: 224 sheet: -1.57 (0.48), residues: 86 loop : -1.62 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 80 HIS 0.004 0.001 HIS Y 41 PHE 0.014 0.002 PHE Y 26 TYR 0.011 0.002 TYR T 84 ARG 0.005 0.001 ARG Y 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1014 Ramachandran restraints generated. 507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 100 MET cc_start: 0.9063 (mtt) cc_final: 0.8667 (mtp) REVERT: E 199 MET cc_start: 0.9173 (mtm) cc_final: 0.8480 (ptm) REVERT: Y 1 MET cc_start: 0.8564 (tpt) cc_final: 0.8026 (tpp) REVERT: Y 7 ARG cc_start: 0.9173 (ptp-110) cc_final: 0.8570 (ttp80) REVERT: T 11 LEU cc_start: 0.8848 (pt) cc_final: 0.8626 (pp) REVERT: T 32 LEU cc_start: 0.8298 (mt) cc_final: 0.8012 (mp) REVERT: T 51 PHE cc_start: 0.8820 (m-80) cc_final: 0.8454 (m-80) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.4037 time to fit residues: 37.4986 Evaluate side-chains 46 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 13 optimal weight: 10.9990 chunk 25 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 93 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.047344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.033774 restraints weight = 225400.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.034695 restraints weight = 95307.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.035215 restraints weight = 62339.328| |-----------------------------------------------------------------------------| r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.9816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 19762 Z= 0.455 Angle : 0.955 27.492 29894 Z= 0.459 Chirality : 0.055 1.900 3913 Planarity : 0.006 0.059 1349 Dihedral : 26.178 160.393 10573 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 53.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: -2.33 (0.34), residues: 507 helix: -0.73 (0.32), residues: 225 sheet: -2.43 (0.44), residues: 97 loop : -1.84 (0.41), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP T 80 HIS 0.005 0.002 HIS 2 16 PHE 0.020 0.003 PHE Y 26 TYR 0.012 0.003 TYR T 84 ARG 0.010 0.001 ARG Y 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2204.97 seconds wall clock time: 42 minutes 33.29 seconds (2553.29 seconds total)