Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 16:05:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouz_17206/07_2023/8ouz_17206_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouz_17206/07_2023/8ouz_17206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouz_17206/07_2023/8ouz_17206.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouz_17206/07_2023/8ouz_17206.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouz_17206/07_2023/8ouz_17206_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouz_17206/07_2023/8ouz_17206_trim_updated.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 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: 7 Type Number sf(0) Gaussians P 8 5.49 5 Mg 3 5.21 5 S 49 5.16 5 C 4603 2.51 5 N 1267 2.21 5 O 1519 1.98 5 H 7373 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 14822 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1132 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "B" Number of atoms: 4960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4960 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 10, 'TRANS': 301} Chain breaks: 2 Chain: "C" Number of atoms: 4722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 4722 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 7, 'TRANS': 300} Chain breaks: 1 Chain: "D" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3774 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Time building chain proxies: 6.10, per 1000 atoms: 0.41 Number of scatterers: 14822 At special positions: 0 Unit cell: (93.7125, 103.275, 93.7125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 49 16.00 P 8 15.00 Mg 3 11.99 O 1519 8.00 N 1267 7.00 C 4603 6.00 H 7373 1.00 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: 11.87 Conformation dependent library (CDL) restraints added in 1.2 seconds 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1720 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 4 sheets defined 44.3% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 6 through 9 No H-bonds generated for 'chain 'A' and resid 6 through 9' Processing helix chain 'A' and resid 13 through 22 removed outlier: 3.965A pdb=" N HIS A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 31 Processing helix chain 'A' and resid 35 through 42 Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.664A pdb=" N ALA A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'B' and resid 14 through 16 No H-bonds generated for 'chain 'B' and resid 14 through 16' Processing helix chain 'B' and resid 21 through 29 Processing helix chain 'B' and resid 35 through 38 Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 54 through 65 Processing helix chain 'B' and resid 87 through 96 Processing helix chain 'B' and resid 105 through 111 Processing helix chain 'B' and resid 131 through 143 removed outlier: 4.388A pdb=" N GLN B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 166 through 186 removed outlier: 3.595A pdb=" N GLU B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LYS B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 198 removed outlier: 3.887A pdb=" N ASP B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 207 removed outlier: 3.666A pdb=" N HIS B 207 " --> pdb=" O ASN B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 232 Proline residue: B 227 - end of helix removed outlier: 3.811A pdb=" N GLU B 232 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 Processing helix chain 'B' and resid 267 through 275 Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 36 through 41 Processing helix chain 'C' and resid 47 through 61 Processing helix chain 'C' and resid 68 through 78 removed outlier: 3.715A pdb=" N THR C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 92 Processing helix chain 'C' and resid 113 through 126 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 157 through 164 Processing helix chain 'C' and resid 175 through 191 Processing helix chain 'C' and resid 208 through 215 Proline residue: C 214 - end of helix Processing helix chain 'C' and resid 222 through 239 Processing helix chain 'C' and resid 266 through 270 removed outlier: 3.804A pdb=" N PHE C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 270' Processing helix chain 'D' and resid 24 through 27 No H-bonds generated for 'chain 'D' and resid 24 through 27' Processing helix chain 'D' and resid 54 through 66 Processing helix chain 'D' and resid 69 through 71 No H-bonds generated for 'chain 'D' and resid 69 through 71' Processing helix chain 'D' and resid 89 through 99 Processing helix chain 'D' and resid 105 through 114 removed outlier: 3.886A pdb=" N ARG D 114 " --> pdb=" O TYR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 139 removed outlier: 3.985A pdb=" N GLU D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N SER D 135 " --> pdb=" O TYR D 131 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 161 Processing helix chain 'D' and resid 166 through 169 No H-bonds generated for 'chain 'D' and resid 166 through 169' Processing helix chain 'D' and resid 171 through 186 Processing helix chain 'D' and resid 229 through 234 removed outlier: 4.071A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 336 through 338 removed outlier: 6.644A pdb=" N ARG B 312 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 280 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE B 123 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU B 282 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU B 154 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL B 239 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B 156 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N VAL B 241 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE B 158 " --> pdb=" O VAL B 241 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 340 through 342 Processing sheet with id= C, first strand: chain 'C' and resid 306 through 309 removed outlier: 6.230A pdb=" N ARG C 275 " --> pdb=" O ALA C 296 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 245 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE C 105 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL C 247 " --> pdb=" O ILE C 105 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 276 through 279 removed outlier: 3.548A pdb=" N HIS D 237 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY D 48 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N GLU D 77 " --> pdb=" O CYS D 144 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU D 146 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU D 79 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU D 148 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE D 81 " --> pdb=" O LEU D 148 " (cutoff:3.500A) 301 hydrogen bonds defined for protein. 870 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.41 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: 0.84 - 1.03: 7345 1.03 - 1.23: 31 1.23 - 1.42: 2984 1.42 - 1.62: 4363 1.62 - 1.81: 70 Bond restraints: 14793 Sorted by residual: bond pdb=" N GLY D 20 " pdb=" CA GLY D 20 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.43e+00 bond pdb=" N GLY C 2 " pdb=" CA GLY C 2 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.96e+00 bond pdb=" N GLN B 11 " pdb=" CA GLN B 11 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" N LYS A 4 " pdb=" CA LYS A 4 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" N GLY D 20 " pdb=" H GLY D 20 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.40e+00 ... (remaining 14788 not shown) Histogram of bond angle deviations from ideal: 100.46 - 108.33: 4275 108.33 - 116.20: 15242 116.20 - 124.07: 6276 124.07 - 131.94: 947 131.94 - 139.80: 14 Bond angle restraints: 26754 Sorted by residual: angle pdb=" C3' ATP D 301 " pdb=" C2' ATP D 301 " pdb=" O2' ATP D 301 " ideal model delta sigma weight residual 111.83 104.67 7.16 2.67e+00 1.40e-01 7.20e+00 angle pdb=" C3' ATP C 401 " pdb=" C4' ATP C 401 " pdb=" C5' ATP C 401 " ideal model delta sigma weight residual 115.19 110.70 4.49 1.76e+00 3.23e-01 6.50e+00 angle pdb=" C3' ATP D 301 " pdb=" C4' ATP D 301 " pdb=" C5' ATP D 301 " ideal model delta sigma weight residual 115.19 110.75 4.44 1.76e+00 3.23e-01 6.37e+00 angle pdb=" C2' ATP D 301 " pdb=" C3' ATP D 301 " pdb=" O3' ATP D 301 " ideal model delta sigma weight residual 111.83 105.24 6.59 2.67e+00 1.40e-01 6.10e+00 angle pdb=" C3' ATP D 301 " pdb=" C4' ATP D 301 " pdb=" O4' ATP D 301 " ideal model delta sigma weight residual 105.22 102.02 3.20 1.30e+00 5.94e-01 6.09e+00 ... (remaining 26749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.10: 5637 29.10 - 58.20: 197 58.20 - 87.29: 26 87.29 - 116.39: 3 116.39 - 145.49: 1 Dihedral angle restraints: 5864 sinusoidal: 2829 harmonic: 3035 Sorted by residual: dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 85.49 -145.49 1 2.00e+01 2.50e-03 4.38e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -171.86 111.86 1 2.00e+01 2.50e-03 3.29e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 36.74 -96.74 1 2.00e+01 2.50e-03 2.68e+01 ... (remaining 5861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1042 0.060 - 0.119: 111 0.119 - 0.179: 17 0.179 - 0.239: 0 0.239 - 0.298: 6 Chirality restraints: 1176 Sorted by residual: chirality pdb=" C2' ATP D 301 " pdb=" C1' ATP D 301 " pdb=" C3' ATP D 301 " pdb=" O2' ATP D 301 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C3' ATP D 301 " pdb=" C2' ATP D 301 " pdb=" C4' ATP D 301 " pdb=" O3' ATP D 301 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C2' ATP C 401 " pdb=" C1' ATP C 401 " pdb=" C3' ATP C 401 " pdb=" O2' ATP C 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1173 not shown) Planarity restraints: 2146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 34 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.58e+00 pdb=" N PRO A 35 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 35 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 35 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 307 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.51e+00 pdb=" CD GLU C 307 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLU C 307 " -0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU C 307 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 263 " -0.005 2.00e-02 2.50e+03 9.70e-03 9.41e-01 pdb=" C ASN B 263 " 0.017 2.00e-02 2.50e+03 pdb=" O ASN B 263 " -0.006 2.00e-02 2.50e+03 pdb=" N GLY B 264 " -0.006 2.00e-02 2.50e+03 ... (remaining 2143 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 392 2.13 - 2.75: 27133 2.75 - 3.37: 42432 3.37 - 3.98: 55325 3.98 - 4.60: 86968 Nonbonded interactions: 212250 Sorted by model distance: nonbonded pdb=" HG1 THR B 132 " pdb="MG MG B 402 " model vdw 1.513 1.700 nonbonded pdb=" OE1 GLN D 200 " pdb=" H GLN D 200 " model vdw 1.534 1.850 nonbonded pdb=" HG1 THR D 55 " pdb="MG MG D 302 " model vdw 1.548 1.700 nonbonded pdb=" O ILE D 66 " pdb="HH21 ARG D 114 " model vdw 1.652 1.850 nonbonded pdb=" OE1 GLU C 104 " pdb="HH11 ARG C 275 " model vdw 1.652 1.850 ... (remaining 212245 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 0.240 Extract box with map and model: 7.850 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 47.600 Find NCS groups from input model: 0.280 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:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 : 0.003 0.041 7420 Z= 0.174 Angle : 0.561 7.161 10033 Z= 0.290 Chirality : 0.044 0.298 1176 Planarity : 0.003 0.031 1256 Dihedral : 15.858 145.487 2743 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 1.00 % 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: 1.04 (0.28), residues: 906 helix: 1.66 (0.26), residues: 423 sheet: 0.45 (0.41), residues: 163 loop : -0.43 (0.33), residues: 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 100 average time/residue: 2.9338 time to fit residues: 308.7340 Evaluate side-chains 88 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 1 average time/residue: 0.2644 time to fit residues: 1.8647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 GLN ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7420 Z= 0.242 Angle : 0.545 7.261 10033 Z= 0.282 Chirality : 0.040 0.140 1176 Planarity : 0.003 0.039 1256 Dihedral : 7.003 120.704 1006 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 2.37 % 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: 0.78 (0.28), residues: 906 helix: 1.38 (0.25), residues: 425 sheet: 0.36 (0.41), residues: 165 loop : -0.49 (0.34), residues: 316 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 104 average time/residue: 2.5539 time to fit residues: 281.7621 Evaluate side-chains 100 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 1.278 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.1553 time to fit residues: 1.9757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 7420 Z= 0.305 Angle : 0.596 7.644 10033 Z= 0.310 Chirality : 0.042 0.142 1176 Planarity : 0.004 0.036 1256 Dihedral : 6.718 101.227 1006 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.28), residues: 906 helix: 1.11 (0.25), residues: 424 sheet: 0.29 (0.41), residues: 165 loop : -0.63 (0.33), residues: 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 107 average time/residue: 2.6184 time to fit residues: 296.6993 Evaluate side-chains 104 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 1.187 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.1625 time to fit residues: 2.0838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 GLN ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 7420 Z= 0.214 Angle : 0.536 7.069 10033 Z= 0.275 Chirality : 0.039 0.136 1176 Planarity : 0.003 0.033 1256 Dihedral : 5.985 84.375 1006 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 2.87 % 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: 0.63 (0.28), residues: 906 helix: 1.30 (0.25), residues: 425 sheet: 0.28 (0.41), residues: 165 loop : -0.61 (0.33), residues: 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 91 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 109 average time/residue: 2.7098 time to fit residues: 312.0706 Evaluate side-chains 104 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.1857 time to fit residues: 2.3551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 GLN ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 7420 Z= 0.206 Angle : 0.530 6.708 10033 Z= 0.271 Chirality : 0.039 0.135 1176 Planarity : 0.003 0.032 1256 Dihedral : 5.637 74.868 1006 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 2.24 % 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: 0.72 (0.28), residues: 906 helix: 1.41 (0.26), residues: 424 sheet: 0.27 (0.41), residues: 165 loop : -0.61 (0.33), residues: 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 107 average time/residue: 2.5910 time to fit residues: 294.2200 Evaluate side-chains 105 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 1.241 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.1919 time to fit residues: 2.5282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 7420 Z= 0.189 Angle : 0.523 6.250 10033 Z= 0.266 Chirality : 0.039 0.135 1176 Planarity : 0.003 0.031 1256 Dihedral : 5.261 63.438 1006 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 2.37 % 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 (0.28), residues: 906 helix: 1.49 (0.26), residues: 425 sheet: 0.31 (0.41), residues: 163 loop : -0.62 (0.33), residues: 318 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 102 average time/residue: 2.5499 time to fit residues: 276.7603 Evaluate side-chains 101 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.1660 time to fit residues: 2.0995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7420 Z= 0.220 Angle : 0.540 6.645 10033 Z= 0.276 Chirality : 0.040 0.137 1176 Planarity : 0.003 0.032 1256 Dihedral : 5.209 50.402 1006 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 2.49 % 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: 0.72 (0.28), residues: 906 helix: 1.41 (0.26), residues: 424 sheet: 0.29 (0.41), residues: 165 loop : -0.63 (0.33), residues: 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 1.187 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 107 average time/residue: 2.4985 time to fit residues: 283.9351 Evaluate side-chains 99 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.1556 time to fit residues: 1.9305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 GLN D 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 7420 Z= 0.201 Angle : 0.534 6.052 10033 Z= 0.272 Chirality : 0.039 0.135 1176 Planarity : 0.003 0.032 1256 Dihedral : 5.070 44.645 1006 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 2.12 % 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: 0.75 (0.28), residues: 906 helix: 1.45 (0.26), residues: 425 sheet: 0.27 (0.40), residues: 165 loop : -0.61 (0.33), residues: 316 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 1.195 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 15 residues processed: 105 average time/residue: 2.5791 time to fit residues: 287.0361 Evaluate side-chains 105 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.1894 time to fit residues: 2.4799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 52 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 7420 Z= 0.166 Angle : 0.509 6.257 10033 Z= 0.257 Chirality : 0.038 0.134 1176 Planarity : 0.003 0.031 1256 Dihedral : 4.753 40.819 1006 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 2.00 % 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: 0.91 (0.28), residues: 906 helix: 1.63 (0.26), residues: 425 sheet: 0.33 (0.40), residues: 163 loop : -0.59 (0.33), residues: 318 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 1.215 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 15 residues processed: 101 average time/residue: 2.5904 time to fit residues: 277.5217 Evaluate side-chains 106 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.2114 time to fit residues: 2.2879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 7420 Z= 0.190 Angle : 0.523 6.157 10033 Z= 0.266 Chirality : 0.039 0.135 1176 Planarity : 0.003 0.032 1256 Dihedral : 4.863 39.582 1006 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 2.00 % 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: 0.87 (0.28), residues: 906 helix: 1.59 (0.26), residues: 425 sheet: 0.30 (0.40), residues: 165 loop : -0.60 (0.33), residues: 316 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 1.138 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 15 residues processed: 106 average time/residue: 2.6023 time to fit residues: 291.9719 Evaluate side-chains 105 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.1641 time to fit residues: 2.1240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.144288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.114668 restraints weight = 24862.867| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.95 r_work: 0.3438 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7420 Z= 0.223 Angle : 0.547 6.162 10033 Z= 0.279 Chirality : 0.040 0.137 1176 Planarity : 0.003 0.039 1256 Dihedral : 5.002 38.543 1006 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 2.12 % 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: 0.75 (0.28), residues: 906 helix: 1.46 (0.26), residues: 424 sheet: 0.30 (0.40), residues: 165 loop : -0.63 (0.33), residues: 317 =============================================================================== Job complete usr+sys time: 6122.08 seconds wall clock time: 107 minutes 35.32 seconds (6455.32 seconds total)