Starting phenix.real_space_refine on Fri Dec 8 08:16:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upi_26667/12_2023/7upi_26667_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upi_26667/12_2023/7upi_26667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upi_26667/12_2023/7upi_26667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upi_26667/12_2023/7upi_26667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upi_26667/12_2023/7upi_26667_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upi_26667/12_2023/7upi_26667_updated.pdb" } resolution = 2.89 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= 0.001 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: 8 Type Number sf(0) Gaussians Mn 2 7.51 5 P 3 5.49 5 Mg 1 5.21 5 S 40 5.16 5 Cl 1 4.86 5 C 4937 2.51 5 N 1324 2.21 5 O 1467 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-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7775 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 165} Chain: "B" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2356 Classifications: {'peptide': 293} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 279} Chain: "C" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3977 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 27, 'TRANS': 477} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 1, ' MN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.59, per 1000 atoms: 0.59 Number of scatterers: 7775 At special positions: 0 Unit cell: (101.46, 92.916, 92.916, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Mn 2 24.99 Cl 1 17.00 S 40 16.00 P 3 15.00 Mg 1 11.99 O 1467 8.00 N 1324 7.00 C 4937 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: 3.12 Conformation dependent library (CDL) restraints added in 1.5 seconds 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 6 sheets defined 28.7% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 26 through 34 Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 97 through 114 removed outlier: 3.536A pdb=" N VAL A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP A 104 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 148 Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.950A pdb=" N PHE A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 17 Processing helix chain 'B' and resid 32 through 47 Processing helix chain 'B' and resid 69 through 79 Processing helix chain 'B' and resid 100 through 113 Processing helix chain 'B' and resid 128 through 134 removed outlier: 3.572A pdb=" N ILE B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 143 Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.868A pdb=" N CYS B 158 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 200 through 206 Processing helix chain 'B' and resid 229 through 239 Processing helix chain 'B' and resid 272 through 274 No H-bonds generated for 'chain 'B' and resid 272 through 274' Processing helix chain 'C' and resid 88 through 100 Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 140 through 144 Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 186 through 190 removed outlier: 3.658A pdb=" N ARG C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 186 through 190' Processing helix chain 'C' and resid 209 through 213 removed outlier: 3.560A pdb=" N LYS C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.534A pdb=" N GLY C 235 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.968A pdb=" N GLY C 281 " --> pdb=" O ASP C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 326 through 329 No H-bonds generated for 'chain 'C' and resid 326 through 329' Processing helix chain 'C' and resid 351 through 354 Processing helix chain 'C' and resid 396 through 400 removed outlier: 4.599A pdb=" N GLY C 399 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 423 removed outlier: 3.584A pdb=" N SER C 422 " --> pdb=" O GLU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 446 No H-bonds generated for 'chain 'C' and resid 444 through 446' Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 488 through 492 removed outlier: 3.833A pdb=" N GLY C 491 " --> pdb=" O ARG C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 removed outlier: 3.585A pdb=" N GLY C 514 " --> pdb=" O GLU C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 539 Processing helix chain 'C' and resid 558 through 563 Processing helix chain 'C' and resid 565 through 575 Processing sheet with id= A, first strand: chain 'A' and resid 151 through 154 removed outlier: 6.820A pdb=" N PHE A 88 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL A 124 " --> pdb=" O PHE A 88 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE A 90 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ASN A 126 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TYR A 92 " --> pdb=" O ASN A 126 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 52 through 55 removed outlier: 6.889A pdb=" N ALA B 162 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU B 55 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE B 164 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 243 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N CYS B 172 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N CYS B 245 " --> pdb=" O CYS B 172 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 118 through 120 removed outlier: 6.221A pdb=" N TYR B 87 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LYS B 60 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 216 through 218 Processing sheet with id= E, first strand: chain 'C' and resid 65 through 68 Processing sheet with id= F, first strand: chain 'C' and resid 104 through 106 removed outlier: 6.430A pdb=" N GLU C 127 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR C 150 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N MET C 173 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR C 196 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N MET C 219 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR C 242 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASN C 265 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ARG C 288 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLU C 311 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER C 335 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER C 359 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS C 383 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU C 406 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL C 429 " --> pdb=" O LEU C 407 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLU C 452 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LYS C 475 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N HIS C 498 " --> pdb=" O LEU C 476 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU C 521 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE C 545 " --> pdb=" O LEU C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 185 hydrogen bonds defined for protein. 462 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: 2.48 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1680 1.33 - 1.45: 1573 1.45 - 1.57: 4598 1.57 - 1.69: 5 1.69 - 1.81: 59 Bond restraints: 7915 Sorted by residual: bond pdb=" N VAL A 39 " pdb=" CA VAL A 39 " ideal model delta sigma weight residual 1.460 1.487 -0.027 7.30e-03 1.88e+04 1.37e+01 bond pdb=" N GLN B 249 " pdb=" CA GLN B 249 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 6.90e+00 bond pdb=" N HIS B 248 " pdb=" CA HIS B 248 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.12e+00 bond pdb=" C LYS A 127 " pdb=" N VAL A 128 " ideal model delta sigma weight residual 1.336 1.365 -0.028 1.17e-02 7.31e+03 5.82e+00 bond pdb=" C2 GTP A 201 " pdb=" N3 GTP A 201 " ideal model delta sigma weight residual 1.380 1.332 0.048 2.00e-02 2.50e+03 5.67e+00 ... (remaining 7910 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.56: 251 106.56 - 113.41: 4398 113.41 - 120.26: 2739 120.26 - 127.11: 3255 127.11 - 133.96: 81 Bond angle restraints: 10724 Sorted by residual: angle pdb=" PB GTP A 201 " pdb=" O3B GTP A 201 " pdb=" PG GTP A 201 " ideal model delta sigma weight residual 120.50 132.61 -12.11 3.00e+00 1.11e-01 1.63e+01 angle pdb=" PA GTP A 201 " pdb=" O3A GTP A 201 " pdb=" PB GTP A 201 " ideal model delta sigma weight residual 120.50 131.86 -11.36 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C1' GTP A 201 " pdb=" C2' GTP A 201 " pdb=" C3' GTP A 201 " ideal model delta sigma weight residual 111.00 99.71 11.29 3.00e+00 1.11e-01 1.42e+01 angle pdb=" CA GLN B 68 " pdb=" C GLN B 68 " pdb=" O GLN B 68 " ideal model delta sigma weight residual 122.41 118.10 4.31 1.21e+00 6.83e-01 1.27e+01 angle pdb=" C TYR B 70 " pdb=" CA TYR B 70 " pdb=" CB TYR B 70 " ideal model delta sigma weight residual 110.67 117.48 -6.81 1.92e+00 2.71e-01 1.26e+01 ... (remaining 10719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.99: 4829 28.99 - 57.98: 25 57.98 - 86.97: 1 86.97 - 115.97: 2 115.97 - 144.96: 4 Dihedral angle restraints: 4861 sinusoidal: 2022 harmonic: 2839 Sorted by residual: dihedral pdb=" C8 GTP A 201 " pdb=" C1' GTP A 201 " pdb=" N9 GTP A 201 " pdb=" O4' GTP A 201 " ideal model delta sinusoidal sigma weight residual 104.59 -40.36 144.96 1 2.00e+01 2.50e-03 4.36e+01 dihedral pdb=" O3B GTP A 201 " pdb=" O3A GTP A 201 " pdb=" PB GTP A 201 " pdb=" PA GTP A 201 " ideal model delta sinusoidal sigma weight residual -68.92 74.77 -143.69 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" C5' GTP A 201 " pdb=" O5' GTP A 201 " pdb=" PA GTP A 201 " pdb=" O3A GTP A 201 " ideal model delta sinusoidal sigma weight residual 69.27 -60.23 129.50 1 2.00e+01 2.50e-03 3.93e+01 ... (remaining 4858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1110 0.059 - 0.118: 117 0.118 - 0.177: 8 0.177 - 0.236: 3 0.236 - 0.296: 1 Chirality restraints: 1239 Sorted by residual: chirality pdb=" C3' GTP A 201 " pdb=" C2' GTP A 201 " pdb=" C4' GTP A 201 " pdb=" O3' GTP A 201 " both_signs ideal model delta sigma weight residual False -2.47 -2.77 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB VAL A 128 " pdb=" CA VAL A 128 " pdb=" CG1 VAL A 128 " pdb=" CG2 VAL A 128 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA VAL A 128 " pdb=" N VAL A 128 " pdb=" C VAL A 128 " pdb=" CB VAL A 128 " both_signs ideal model delta sigma weight residual False 2.44 2.25 0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 1236 not shown) Planarity restraints: 1376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 70 " -0.029 2.00e-02 2.50e+03 1.69e-02 5.71e+00 pdb=" CG TYR B 70 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 70 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 70 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 70 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 70 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 70 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 70 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 67 " 0.005 2.00e-02 2.50e+03 1.11e-02 1.24e+00 pdb=" C GLY B 67 " -0.019 2.00e-02 2.50e+03 pdb=" O GLY B 67 " 0.007 2.00e-02 2.50e+03 pdb=" N GLN B 68 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 70 " -0.005 2.00e-02 2.50e+03 1.10e-02 1.21e+00 pdb=" C TYR B 70 " 0.019 2.00e-02 2.50e+03 pdb=" O TYR B 70 " -0.007 2.00e-02 2.50e+03 pdb=" N ASP B 71 " -0.007 2.00e-02 2.50e+03 ... (remaining 1373 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 16 2.45 - 3.07: 5141 3.07 - 3.68: 11318 3.68 - 4.29: 18468 4.29 - 4.90: 30428 Nonbonded interactions: 65371 Sorted by model distance: nonbonded pdb=" OD1 ASN B 124 " pdb="MN MN B 401 " model vdw 1.843 2.320 nonbonded pdb=" OD2 ASP B 92 " pdb="MN MN B 401 " model vdw 1.934 2.320 nonbonded pdb=" OG SER A 27 " pdb="MG MG A 202 " model vdw 1.984 2.170 nonbonded pdb=" O2G GTP A 201 " pdb="MG MG A 202 " model vdw 1.984 2.170 nonbonded pdb=" NE2 HIS B 66 " pdb="MN MN B 402 " model vdw 2.052 2.400 ... (remaining 65366 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: 0.960 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: 0.000 Extract box with map and model: 4.120 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.930 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 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 : 0.002 0.071 7915 Z= 0.170 Angle : 0.547 12.107 10724 Z= 0.271 Chirality : 0.041 0.296 1239 Planarity : 0.003 0.027 1376 Dihedral : 9.087 144.958 3017 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.12 (0.28), residues: 964 helix: -0.18 (0.30), residues: 326 sheet: -0.36 (0.39), residues: 196 loop : 0.38 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 149 HIS 0.003 0.000 HIS B 248 PHE 0.005 0.001 PHE B 118 TYR 0.036 0.001 TYR B 70 ARG 0.001 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 1.3873 time to fit residues: 98.5912 Evaluate side-chains 42 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 0.0870 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7915 Z= 0.208 Angle : 0.469 8.466 10724 Z= 0.235 Chirality : 0.040 0.131 1239 Planarity : 0.003 0.054 1376 Dihedral : 9.721 147.363 1055 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.68 % Allowed : 5.09 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.05 (0.28), residues: 964 helix: -0.06 (0.31), residues: 325 sheet: -0.50 (0.38), residues: 196 loop : 0.47 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 401 HIS 0.003 0.001 HIS B 239 PHE 0.015 0.001 PHE C 535 TYR 0.011 0.001 TYR B 70 ARG 0.008 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 1.016 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 47 average time/residue: 1.3014 time to fit residues: 65.6880 Evaluate side-chains 40 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.2941 time to fit residues: 2.5833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 59 optimal weight: 0.0020 chunk 24 optimal weight: 0.0010 chunk 87 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7915 Z= 0.204 Angle : 0.460 8.422 10724 Z= 0.231 Chirality : 0.039 0.131 1239 Planarity : 0.003 0.030 1376 Dihedral : 9.216 145.709 1055 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.57 % Allowed : 5.77 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.13 (0.28), residues: 964 helix: -0.12 (0.31), residues: 325 sheet: -0.65 (0.38), residues: 191 loop : 0.46 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 401 HIS 0.002 0.001 HIS B 239 PHE 0.006 0.001 PHE C 398 TYR 0.015 0.001 TYR B 70 ARG 0.005 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 44 average time/residue: 1.3448 time to fit residues: 63.6167 Evaluate side-chains 37 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.3522 time to fit residues: 2.8236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 41 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7915 Z= 0.201 Angle : 0.477 10.422 10724 Z= 0.235 Chirality : 0.039 0.128 1239 Planarity : 0.003 0.033 1376 Dihedral : 8.989 146.471 1055 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.02 % Allowed : 5.54 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.13 (0.28), residues: 964 helix: -0.17 (0.31), residues: 326 sheet: -0.64 (0.38), residues: 191 loop : 0.50 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 149 HIS 0.002 0.001 HIS B 239 PHE 0.007 0.001 PHE C 398 TYR 0.013 0.001 TYR B 70 ARG 0.004 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 1.056 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 0 residues processed: 45 average time/residue: 1.5884 time to fit residues: 76.0812 Evaluate side-chains 37 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.0980 chunk 79 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7915 Z= 0.318 Angle : 0.529 11.383 10724 Z= 0.261 Chirality : 0.041 0.167 1239 Planarity : 0.003 0.035 1376 Dihedral : 8.863 148.133 1055 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.90 % Allowed : 5.77 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.20 (0.28), residues: 964 helix: -0.26 (0.31), residues: 328 sheet: -0.63 (0.38), residues: 196 loop : 0.48 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 401 HIS 0.004 0.001 HIS B 239 PHE 0.007 0.001 PHE A 106 TYR 0.015 0.001 TYR B 70 ARG 0.002 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 1.020 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 44 average time/residue: 1.4343 time to fit residues: 67.8086 Evaluate side-chains 38 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.3453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 92 optimal weight: 0.0070 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7915 Z= 0.170 Angle : 0.494 12.372 10724 Z= 0.244 Chirality : 0.039 0.155 1239 Planarity : 0.003 0.039 1376 Dihedral : 8.492 146.551 1055 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.90 % Allowed : 6.22 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.28), residues: 964 helix: -0.26 (0.31), residues: 328 sheet: -0.70 (0.39), residues: 191 loop : 0.48 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 401 HIS 0.004 0.001 HIS B 239 PHE 0.009 0.001 PHE C 398 TYR 0.013 0.001 TYR B 70 ARG 0.002 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 42 average time/residue: 1.3396 time to fit residues: 60.6088 Evaluate side-chains 40 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.0857 time to fit residues: 2.4721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.0070 chunk 52 optimal weight: 0.0770 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7915 Z= 0.120 Angle : 0.482 13.459 10724 Z= 0.235 Chirality : 0.039 0.130 1239 Planarity : 0.003 0.035 1376 Dihedral : 7.986 142.658 1055 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.23 % Allowed : 6.79 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.28), residues: 964 helix: -0.28 (0.31), residues: 325 sheet: -0.72 (0.38), residues: 194 loop : 0.56 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 401 HIS 0.002 0.000 HIS B 248 PHE 0.009 0.001 PHE C 398 TYR 0.011 0.001 TYR B 70 ARG 0.002 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 1.051 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 42 average time/residue: 1.4600 time to fit residues: 65.5283 Evaluate side-chains 38 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.3771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7915 Z= 0.272 Angle : 0.525 11.664 10724 Z= 0.256 Chirality : 0.040 0.134 1239 Planarity : 0.003 0.032 1376 Dihedral : 8.093 143.099 1055 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.68 % Allowed : 7.01 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.24 (0.28), residues: 964 helix: -0.35 (0.31), residues: 328 sheet: -0.71 (0.39), residues: 191 loop : 0.53 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 206 HIS 0.004 0.001 HIS B 239 PHE 0.013 0.001 PHE C 535 TYR 0.013 0.001 TYR B 70 ARG 0.002 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 1.016 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 40 average time/residue: 1.3431 time to fit residues: 57.9151 Evaluate side-chains 37 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.4245 time to fit residues: 2.9062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 0.0970 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7915 Z= 0.175 Angle : 0.528 15.355 10724 Z= 0.251 Chirality : 0.040 0.159 1239 Planarity : 0.003 0.032 1376 Dihedral : 7.955 141.956 1055 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.34 % Allowed : 7.35 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.28 (0.28), residues: 964 helix: -0.42 (0.30), residues: 325 sheet: -0.72 (0.39), residues: 191 loop : 0.53 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 206 HIS 0.004 0.001 HIS B 239 PHE 0.010 0.001 PHE C 398 TYR 0.011 0.001 TYR B 70 ARG 0.002 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.993 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 1.3616 time to fit residues: 58.7327 Evaluate side-chains 37 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.2690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.0770 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7915 Z= 0.180 Angle : 0.533 13.482 10724 Z= 0.255 Chirality : 0.040 0.146 1239 Planarity : 0.003 0.036 1376 Dihedral : 7.870 141.166 1055 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.23 % Allowed : 7.47 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.27 (0.28), residues: 964 helix: -0.42 (0.30), residues: 325 sheet: -0.72 (0.39), residues: 191 loop : 0.53 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 206 HIS 0.004 0.001 HIS B 239 PHE 0.014 0.001 PHE C 535 TYR 0.011 0.001 TYR B 70 ARG 0.001 0.000 ARG A 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 1.075 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 1.4426 time to fit residues: 57.3360 Evaluate side-chains 36 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.3861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 0.2980 chunk 66 optimal weight: 0.0980 chunk 4 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.047773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.036999 restraints weight = 26907.963| |-----------------------------------------------------------------------------| r_work (start): 0.2581 rms_B_bonded: 3.35 r_work: 0.2417 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7915 Z= 0.133 Angle : 0.522 13.835 10724 Z= 0.248 Chirality : 0.039 0.137 1239 Planarity : 0.003 0.039 1376 Dihedral : 7.695 139.273 1055 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.11 % Allowed : 7.69 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.22 (0.28), residues: 964 helix: -0.40 (0.30), residues: 325 sheet: -0.68 (0.39), residues: 191 loop : 0.57 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 206 HIS 0.003 0.000 HIS B 239 PHE 0.010 0.001 PHE C 398 TYR 0.010 0.001 TYR B 70 ARG 0.002 0.000 ARG A 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.21 seconds wall clock time: 41 minutes 25.65 seconds (2485.65 seconds total)