Starting phenix.real_space_refine on Fri Nov 17 04:58:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/11_2023/8c9a_16507.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/11_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_16507/11_2023/8c9a_16507.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/11_2023/8c9a_16507.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/11_2023/8c9a_16507.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/11_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 13 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: 11.21, per 1000 atoms: 0.62 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: 11.81 Conformation dependent library (CDL) restraints added in 880.9 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: 9.43 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: 9.50 Time building geometry restraints manager: 12.18 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: 10064 35.82 - 71.63: 278 71.63 - 107.45: 43 107.45 - 143.27: 2 143.27 - 179.09: 3 Dihedral angle restraints: 10390 sinusoidal: 8872 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 10387 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: 1.370 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: 6.720 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 62.530 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.450 ------------------------------------------------------------------------------- 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 : 13.845 179.086 9392 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 *********************** 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 : 1.068 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: 0.3695 time to fit residues: 54.2836 Evaluate side-chains 61 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9102 ------------------------------------------------------------------------------- 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: 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: 10.0000 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: 0.7997 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 19762 Z= 0.289 Angle : 0.732 28.108 29894 Z= 0.351 Chirality : 0.047 1.940 3913 Planarity : 0.005 0.039 1349 Dihedral : 15.565 171.164 8343 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % 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: 0.38 (0.36), residues: 507 helix: 0.95 (0.34), residues: 220 sheet: 0.52 (0.58), residues: 79 loop : -0.52 (0.42), residues: 208 *********************** 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 : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 82 average time/residue: 0.3867 time to fit residues: 45.5823 Evaluate side-chains 58 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1988 time to fit residues: 1.2728 ------------------------------------------------------------------------------- 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: 0.8980 chunk 71 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 15 ASN Y 27 ASN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19762 Z= 0.291 Angle : 0.744 26.672 29894 Z= 0.360 Chirality : 0.048 1.964 3913 Planarity : 0.005 0.053 1349 Dihedral : 17.102 174.621 8343 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 31.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.45 % Allowed : 5.19 % 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: -0.65 (0.36), residues: 507 helix: 0.04 (0.33), residues: 219 sheet: -0.63 (0.58), residues: 85 loop : -0.69 (0.42), residues: 203 *********************** 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 74 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 1.045 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: 2 outliers final: 1 residues processed: 73 average time/residue: 0.3770 time to fit residues: 39.6863 Evaluate side-chains 53 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2061 time to fit residues: 1.3140 ------------------------------------------------------------------------------- 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: 0.9980 chunk 78 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 70 optimal weight: 0.0980 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19762 Z= 0.146 Angle : 0.578 26.970 29894 Z= 0.278 Chirality : 0.042 1.962 3913 Planarity : 0.004 0.027 1349 Dihedral : 16.384 173.895 8343 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.45 % Allowed : 2.93 % 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: -0.19 (0.36), residues: 507 helix: 0.60 (0.34), residues: 217 sheet: -0.07 (0.57), residues: 77 loop : -0.81 (0.41), residues: 213 *********************** 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 82 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 0.990 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: 2 outliers final: 2 residues processed: 81 average time/residue: 0.3822 time to fit residues: 44.5662 Evaluate side-chains 59 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 1.061 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2076 time to fit residues: 1.6452 ------------------------------------------------------------------------------- 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: 20.0000 chunk 45 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 99 optimal weight: 0.7980 chunk 28 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 overall best weight: 6.3590 ------------------------------------------------------------------------------- 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** Y 15 ASN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.7391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 19762 Z= 0.375 Angle : 0.869 27.291 29894 Z= 0.418 Chirality : 0.051 1.942 3913 Planarity : 0.006 0.059 1349 Dihedral : 18.191 172.930 8343 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 44.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % 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: -1.30 (0.34), residues: 507 helix: -0.33 (0.32), residues: 219 sheet: -1.43 (0.51), residues: 92 loop : -0.97 (0.41), residues: 196 *********************** 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 72 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.3746 time to fit residues: 39.2879 Evaluate side-chains 46 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8659 ------------------------------------------------------------------------------- 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: 1.9990 chunk 21 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 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: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 S 61 ASN ** 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: 0.8210 moved from start: 0.7348 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= 0.253 Angle : 0.700 27.060 29894 Z= 0.338 Chirality : 0.047 1.953 3913 Planarity : 0.005 0.035 1349 Dihedral : 17.804 169.231 8343 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 31.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % 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: -1.10 (0.35), residues: 507 helix: 0.06 (0.33), residues: 220 sheet: -1.43 (0.48), residues: 98 loop : -1.07 (0.42), residues: 189 *********************** 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 81 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.3621 time to fit residues: 43.1633 Evaluate side-chains 53 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9101 ------------------------------------------------------------------------------- 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: 9.9990 chunk 62 optimal weight: 30.0000 chunk 93 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 69 optimal weight: 0.0050 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 overall best weight: 4.2002 ------------------------------------------------------------------------------- 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: 0.8226 moved from start: 0.7864 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= 0.263 Angle : 0.720 27.052 29894 Z= 0.348 Chirality : 0.047 1.955 3913 Planarity : 0.005 0.054 1349 Dihedral : 17.962 169.564 8343 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 33.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: -1.34 (0.34), residues: 507 helix: -0.14 (0.33), residues: 217 sheet: -1.49 (0.48), residues: 96 loop : -1.25 (0.41), residues: 194 *********************** 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 78 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.3957 time to fit residues: 45.2441 Evaluate side-chains 48 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8210 ------------------------------------------------------------------------------- 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: 9.9990 chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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** U 52 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: 0.8200 moved from start: 0.7841 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= 0.216 Angle : 0.665 27.015 29894 Z= 0.319 Chirality : 0.045 1.951 3913 Planarity : 0.005 0.042 1349 Dihedral : 17.708 171.091 8343 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 29.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % 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: -1.23 (0.35), residues: 507 helix: 0.06 (0.33), residues: 219 sheet: -1.48 (0.49), residues: 95 loop : -1.33 (0.42), residues: 193 *********************** 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: 1 poor density : 72 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 73 average time/residue: 0.3786 time to fit residues: 39.7185 Evaluate side-chains 46 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1589 time to fit residues: 1.2045 ------------------------------------------------------------------------------- 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: 0.9980 chunk 106 optimal weight: 0.1980 chunk 62 optimal weight: 30.0000 chunk 44 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 40.0000 overall best weight: 3.0386 ------------------------------------------------------------------------------- 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 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: 0.8190 moved from start: 0.7907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19762 Z= 0.201 Angle : 0.648 26.997 29894 Z= 0.310 Chirality : 0.044 1.954 3913 Planarity : 0.004 0.039 1349 Dihedral : 17.472 173.092 8343 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 26.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % 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: -1.23 (0.35), residues: 507 helix: 0.05 (0.33), residues: 219 sheet: -1.51 (0.48), residues: 94 loop : -1.30 (0.42), residues: 194 *********************** 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 : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.3871 time to fit residues: 41.0967 Evaluate side-chains 45 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9059 ------------------------------------------------------------------------------- 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: 1.9990 chunk 51 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.7836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19762 Z= 0.172 Angle : 0.614 26.958 29894 Z= 0.294 Chirality : 0.043 1.958 3913 Planarity : 0.004 0.033 1349 Dihedral : 17.184 174.620 8343 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 23.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -0.90 (0.36), residues: 507 helix: 0.26 (0.35), residues: 219 sheet: -0.92 (0.52), residues: 83 loop : -1.31 (0.42), residues: 205 ********************** 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 73 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3781 time to fit residues: 39.7696 Evaluate side-chains 46 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.935 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8574 ------------------------------------------------------------------------------- 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: 10.0000 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 38 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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 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 = 0.3191 r_free = 0.3191 target = 0.048312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.033698 restraints weight = 208958.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.034692 restraints weight = 86833.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.035236 restraints weight = 56203.770| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.8584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19762 Z= 0.304 Angle : 0.754 27.128 29894 Z= 0.363 Chirality : 0.048 1.939 3913 Planarity : 0.005 0.054 1349 Dihedral : 17.996 165.428 8343 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 36.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % 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: -1.44 (0.35), residues: 507 helix: -0.06 (0.34), residues: 218 sheet: -1.64 (0.48), residues: 94 loop : -1.47 (0.41), residues: 195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2260.84 seconds wall clock time: 43 minutes 47.50 seconds (2627.50 seconds total)