Starting phenix.real_space_refine on Mon Dec 11 13:14:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/12_2023/8c9a_16507.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/12_2023/8c9a_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_16507/12_2023/8c9a_16507.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/12_2023/8c9a_16507.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/12_2023/8c9a_16507.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/12_2023/8c9a_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-1.21rc1-5172/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: 16 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: 10.05, per 1000 atoms: 0.56 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: 10.42 Conformation dependent library (CDL) restraints added in 869.9 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: 8.57 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: 8.77 Time building geometry restraints manager: 10.79 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: 10797 35.82 - 71.63: 1130 71.63 - 107.45: 182 107.45 - 143.27: 2 143.27 - 179.09: 3 Dihedral angle restraints: 12114 sinusoidal: 10596 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 12111 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 6.560 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 57.470 Find NCS groups from input model: 0.330 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: 68.810 ------------------------------------------------------------------------------- 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 : 22.015 179.086 11116 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 : 1.017 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 outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.3663 time to fit residues: 53.2775 Evaluate side-chains 61 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8948 ------------------------------------------------------------------------------- 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: 4.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 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: 4.6388 ------------------------------------------------------------------------------- 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 24 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19762 Z= 0.295 Angle : 0.769 28.290 29894 Z= 0.369 Chirality : 0.048 1.929 3913 Planarity : 0.005 0.041 1349 Dihedral : 23.494 171.076 10067 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 28.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.21 (0.36), residues: 507 helix: 0.75 (0.33), residues: 220 sheet: 0.51 (0.57), residues: 79 loop : -0.57 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP T 80 HIS 0.005 0.001 HIS S 60 PHE 0.017 0.002 PHE Y 26 TYR 0.018 0.002 TYR T 84 ARG 0.005 0.001 ARG E 102 *********************** 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 81 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.3640 time to fit residues: 42.6039 Evaluate side-chains 55 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8954 ------------------------------------------------------------------------------- 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: 8.9990 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 ASN E 30 GLN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19762 Z= 0.182 Angle : 0.592 26.788 29894 Z= 0.283 Chirality : 0.043 1.950 3913 Planarity : 0.004 0.026 1349 Dihedral : 23.518 170.588 10067 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % 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: 0.09 (0.37), residues: 507 helix: 0.76 (0.34), residues: 219 sheet: -0.15 (0.62), residues: 80 loop : -0.48 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP T 80 HIS 0.002 0.001 HIS S 60 PHE 0.011 0.002 PHE Y 26 TYR 0.011 0.002 TYR T 84 ARG 0.004 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 : 0.898 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 outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.3663 time to fit residues: 41.6069 Evaluate side-chains 54 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.835 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8062 ------------------------------------------------------------------------------- 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: 0.7980 chunk 78 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- 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** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN Y 15 ASN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.6434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 19762 Z= 0.334 Angle : 0.807 27.531 29894 Z= 0.389 Chirality : 0.050 1.943 3913 Planarity : 0.005 0.048 1349 Dihedral : 24.400 174.984 10067 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 37.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.23 % Allowed : 4.29 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.79 (0.35), residues: 507 helix: 0.14 (0.33), residues: 217 sheet: -0.89 (0.51), residues: 96 loop : -0.91 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP T 80 HIS 0.005 0.001 HIS Y 41 PHE 0.015 0.002 PHE Y 26 TYR 0.019 0.002 TYR T 84 ARG 0.020 0.001 ARG E 102 *********************** 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 78 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 0.3734 time to fit residues: 41.9308 Evaluate side-chains 48 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.818 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8232 ------------------------------------------------------------------------------- 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: 9.9990 chunk 82 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 GLN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN S 31 GLN ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN Y 27 ASN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.8484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 19762 Z= 0.468 Angle : 0.994 27.573 29894 Z= 0.479 Chirality : 0.056 1.913 3913 Planarity : 0.007 0.066 1349 Dihedral : 25.411 167.095 10067 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 55.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.68 % Allowed : 5.87 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.10 (0.33), residues: 507 helix: -0.93 (0.31), residues: 222 sheet: -1.86 (0.50), residues: 96 loop : -1.44 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP T 80 HIS 0.007 0.002 HIS Y 41 PHE 0.024 0.003 PHE U 94 TYR 0.015 0.003 TYR T 84 ARG 0.013 0.002 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: 3 poor density : 67 time to evaluate : 0.917 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 outliers start: 3 outliers final: 1 residues processed: 69 average time/residue: 0.3858 time to fit residues: 38.0141 Evaluate side-chains 50 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2037 time to fit residues: 1.2297 ------------------------------------------------------------------------------- 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: 6.9990 chunk 21 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 10.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 58 optimal weight: 30.0000 chunk 107 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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** Y 15 ASN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 HIS T 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.8101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 19762 Z= 0.272 Angle : 0.743 27.117 29894 Z= 0.358 Chirality : 0.048 1.944 3913 Planarity : 0.005 0.037 1349 Dihedral : 24.950 165.764 10067 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 35.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: -1.67 (0.33), residues: 507 helix: -0.37 (0.32), residues: 219 sheet: -1.68 (0.49), residues: 97 loop : -1.47 (0.39), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP T 80 HIS 0.004 0.001 HIS Y 41 PHE 0.021 0.002 PHE Y 26 TYR 0.014 0.002 TYR T 84 ARG 0.009 0.001 ARG E 102 *********************** 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 69 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.3921 time to fit residues: 38.7118 Evaluate side-chains 47 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0845 ------------------------------------------------------------------------------- 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: 5.9990 chunk 62 optimal weight: 30.0000 chunk 93 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 69 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 overall best weight: 4.6588 ------------------------------------------------------------------------------- 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 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: 0.8258 moved from start: 0.8519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 19762 Z= 0.289 Angle : 0.759 27.296 29894 Z= 0.365 Chirality : 0.048 1.923 3913 Planarity : 0.005 0.042 1349 Dihedral : 24.966 166.763 10067 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 37.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.34), residues: 507 helix: -0.38 (0.32), residues: 222 sheet: -1.76 (0.49), residues: 96 loop : -1.50 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP T 80 HIS 0.004 0.001 HIS Y 41 PHE 0.017 0.002 PHE Y 26 TYR 0.013 0.002 TYR T 84 ARG 0.010 0.001 ARG Y 47 *********************** 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 70 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.3796 time to fit residues: 38.2053 Evaluate side-chains 49 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.809 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9067 ------------------------------------------------------------------------------- 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: 1.9990 chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.8225 moved from start: 0.8422 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= 0.225 Angle : 0.685 27.121 29894 Z= 0.328 Chirality : 0.046 1.942 3913 Planarity : 0.005 0.044 1349 Dihedral : 24.727 165.361 10067 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 30.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % 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: -1.43 (0.35), residues: 507 helix: -0.01 (0.33), residues: 222 sheet: -1.76 (0.49), residues: 95 loop : -1.47 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.006 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 0.008 0.001 ARG Y 7 *********************** 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 73 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.914 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3836 time to fit residues: 40.3065 Evaluate side-chains 47 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.936 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8976 ------------------------------------------------------------------------------- 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: 5.9990 chunk 106 optimal weight: 0.0970 chunk 62 optimal weight: 30.0000 chunk 44 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.8249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19762 Z= 0.182 Angle : 0.641 27.095 29894 Z= 0.308 Chirality : 0.044 1.943 3913 Planarity : 0.004 0.037 1349 Dihedral : 24.484 165.556 10067 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 25.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: -1.22 (0.35), residues: 507 helix: 0.02 (0.33), residues: 222 sheet: -1.14 (0.57), residues: 70 loop : -1.49 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.005 TRP T 80 HIS 0.003 0.001 HIS Y 41 PHE 0.012 0.002 PHE U 95 TYR 0.009 0.002 TYR T 84 ARG 0.013 0.001 ARG E 114 *********************** 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 74 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.3963 time to fit residues: 42.0790 Evaluate side-chains 45 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.872 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8677 ------------------------------------------------------------------------------- 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: 7.9990 chunk 51 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 9 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- 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: 0.8265 moved from start: 0.8918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19762 Z= 0.305 Angle : 0.765 27.321 29894 Z= 0.369 Chirality : 0.048 1.931 3913 Planarity : 0.005 0.051 1349 Dihedral : 24.887 166.237 10067 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 37.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: -1.63 (0.34), residues: 507 helix: -0.30 (0.32), residues: 222 sheet: -1.27 (0.55), residues: 71 loop : -1.77 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.005 TRP T 80 HIS 0.004 0.001 HIS Y 41 PHE 0.014 0.002 PHE 2 18 TYR 0.010 0.002 TYR T 84 ARG 0.009 0.001 ARG Y 7 ********************** 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 66 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.3997 time to fit residues: 37.6808 Evaluate side-chains 44 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9599 ------------------------------------------------------------------------------- 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: 6.9990 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 80 optimal weight: 0.0000 chunk 5 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.049710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.035952 restraints weight = 211519.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.036981 restraints weight = 82438.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.037515 restraints weight = 51221.625| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.8781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19762 Z= 0.217 Angle : 0.671 27.163 29894 Z= 0.323 Chirality : 0.045 1.944 3913 Planarity : 0.004 0.036 1349 Dihedral : 24.635 164.899 10067 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 29.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: -1.49 (0.34), residues: 507 helix: -0.17 (0.33), residues: 222 sheet: -1.28 (0.54), residues: 71 loop : -1.69 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.004 TRP T 80 HIS 0.004 0.001 HIS Y 41 PHE 0.012 0.002 PHE Y 26 TYR 0.013 0.002 TYR T 84 ARG 0.004 0.001 ARG Y 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2186.32 seconds wall clock time: 42 minutes 29.17 seconds (2549.17 seconds total)