Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:39:50 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9y_0383/11_2022/6n9y_0383.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9y_0383/11_2022/6n9y_0383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9y_0383/11_2022/6n9y_0383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9y_0383/11_2022/6n9y_0383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9y_0383/11_2022/6n9y_0383.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9y_0383/11_2022/6n9y_0383.pdb" } resolution = 4.0 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= 0.009 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4527 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4527 Classifications: {'peptide': 552} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 531} Time building chain proxies: 3.12, per 1000 atoms: 0.69 Number of scatterers: 4527 At special positions: 0 Unit cell: (104.86, 72.76, 112.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 816 8.00 N 798 7.00 C 2874 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: 1.82 Conformation dependent library (CDL) restraints added in 691.7 milliseconds 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1040 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 4 sheets defined 56.3% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 removed outlier: 3.990A pdb=" N TYR A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 25 removed outlier: 4.098A pdb=" N ALA A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ALA A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 38 removed outlier: 4.239A pdb=" N CYS A 37 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 38 " --> pdb=" O ARG A 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 34 through 38' Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 60 through 73 removed outlier: 4.204A pdb=" N TYR A 65 " --> pdb=" O PRO A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 91 removed outlier: 4.235A pdb=" N GLN A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 115 removed outlier: 3.638A pdb=" N LYS A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.613A pdb=" N VAL A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.812A pdb=" N ILE A 145 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 146 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 202 removed outlier: 4.325A pdb=" N GLY A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 194 " --> pdb=" O GLN A 190 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A 195 " --> pdb=" O HIS A 191 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG A 200 " --> pdb=" O ARG A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 230 through 249 removed outlier: 3.545A pdb=" N ALA A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS A 235 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.619A pdb=" N TRP A 307 " --> pdb=" O TRP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 318 removed outlier: 3.533A pdb=" N GLU A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.776A pdb=" N ILE A 328 " --> pdb=" O TRP A 324 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.982A pdb=" N LEU A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 removed outlier: 3.927A pdb=" N LEU A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 422 removed outlier: 3.760A pdb=" N ILE A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 413 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 414 " --> pdb=" O ALA A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.626A pdb=" N PHE A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 443 " --> pdb=" O MET A 439 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP A 447 " --> pdb=" O VAL A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 465 removed outlier: 3.553A pdb=" N ARG A 454 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A 455 " --> pdb=" O LYS A 451 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 491 removed outlier: 4.115A pdb=" N ASP A 487 " --> pdb=" O GLY A 483 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 491 " --> pdb=" O ASP A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 519 removed outlier: 3.757A pdb=" N GLU A 501 " --> pdb=" O GLU A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 550 removed outlier: 4.065A pdb=" N LEU A 541 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 149 Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 162 removed outlier: 3.699A pdb=" N PHE A 159 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER A 161 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ALA A 167 " --> pdb=" O MET A 218 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU A 220 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TYR A 169 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 354 removed outlier: 3.638A pdb=" N CYS A 351 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 353 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 368 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR A 369 " --> pdb=" O ASN A 403 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ASN A 403 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 399 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS A 398 " --> pdb=" O ILE A 395 " (cutoff:3.500A) 166 hydrogen bonds defined for protein. 483 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: 1.34 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1485 1.34 - 1.46: 1065 1.46 - 1.58: 2025 1.58 - 1.70: 0 1.70 - 1.82: 61 Bond restraints: 4636 Sorted by residual: bond pdb=" N ARG A 164 " pdb=" CA ARG A 164 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.17e-02 7.31e+03 7.73e+00 bond pdb=" C SER A 365 " pdb=" N PRO A 366 " ideal model delta sigma weight residual 1.336 1.314 0.022 1.25e-02 6.40e+03 3.17e+00 bond pdb=" CA ALA A 126 " pdb=" C ALA A 126 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.94e+00 bond pdb=" C GLU A 60 " pdb=" O GLU A 60 " ideal model delta sigma weight residual 1.249 1.237 0.011 8.50e-03 1.38e+04 1.80e+00 bond pdb=" N ASN A 40 " pdb=" CA ASN A 40 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.66e+00 ... (remaining 4631 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.87: 90 105.87 - 112.94: 2365 112.94 - 120.01: 1780 120.01 - 127.08: 1966 127.08 - 134.15: 61 Bond angle restraints: 6262 Sorted by residual: angle pdb=" N GLY A 363 " pdb=" CA GLY A 363 " pdb=" C GLY A 363 " ideal model delta sigma weight residual 112.33 118.30 -5.97 1.10e+00 8.26e-01 2.95e+01 angle pdb=" C THR A 204 " pdb=" N CYS A 205 " pdb=" CA CYS A 205 " ideal model delta sigma weight residual 120.51 128.35 -7.84 1.45e+00 4.76e-01 2.92e+01 angle pdb=" C TYR A 163 " pdb=" N ARG A 164 " pdb=" CA ARG A 164 " ideal model delta sigma weight residual 121.19 128.46 -7.27 1.59e+00 3.96e-01 2.09e+01 angle pdb=" C THR A 362 " pdb=" N GLY A 363 " pdb=" CA GLY A 363 " ideal model delta sigma weight residual 120.44 124.68 -4.24 1.09e+00 8.42e-01 1.51e+01 angle pdb=" N ALA A 126 " pdb=" CA ALA A 126 " pdb=" C ALA A 126 " ideal model delta sigma weight residual 110.91 106.37 4.54 1.17e+00 7.31e-01 1.51e+01 ... (remaining 6257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.03: 2355 10.03 - 20.06: 321 20.06 - 30.09: 68 30.09 - 40.12: 23 40.12 - 50.16: 13 Dihedral angle restraints: 2780 sinusoidal: 1161 harmonic: 1619 Sorted by residual: dihedral pdb=" CA ASN A 129 " pdb=" C ASN A 129 " pdb=" N SER A 130 " pdb=" CA SER A 130 " ideal model delta harmonic sigma weight residual -180.00 -138.60 -41.40 0 5.00e+00 4.00e-02 6.86e+01 dihedral pdb=" CA GLU A 255 " pdb=" C GLU A 255 " pdb=" N GLU A 256 " pdb=" CA GLU A 256 " ideal model delta harmonic sigma weight residual -180.00 -146.08 -33.92 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CA THR A 406 " pdb=" C THR A 406 " pdb=" N GLY A 407 " pdb=" CA GLY A 407 " ideal model delta harmonic sigma weight residual -180.00 -147.03 -32.97 0 5.00e+00 4.00e-02 4.35e+01 ... (remaining 2777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 383 0.043 - 0.086: 203 0.086 - 0.129: 49 0.129 - 0.171: 16 0.171 - 0.214: 2 Chirality restraints: 653 Sorted by residual: chirality pdb=" CB ILE A 313 " pdb=" CA ILE A 313 " pdb=" CG1 ILE A 313 " pdb=" CG2 ILE A 313 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE A 166 " pdb=" CA ILE A 166 " pdb=" CG1 ILE A 166 " pdb=" CG2 ILE A 166 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CG LEU A 135 " pdb=" CB LEU A 135 " pdb=" CD1 LEU A 135 " pdb=" CD2 LEU A 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 650 not shown) Planarity restraints: 812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 530 " -0.042 5.00e-02 4.00e+02 6.36e-02 6.46e+00 pdb=" N PRO A 531 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 531 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 531 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 25 " 0.042 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO A 26 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 26 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 26 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 142 " -0.040 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO A 143 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 143 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 143 " -0.034 5.00e-02 4.00e+02 ... (remaining 809 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 892 2.76 - 3.30: 4207 3.30 - 3.83: 7008 3.83 - 4.37: 8154 4.37 - 4.90: 13831 Nonbonded interactions: 34092 Sorted by model distance: nonbonded pdb=" O VAL A 155 " pdb=" OH TYR A 169 " model vdw 2.229 2.440 nonbonded pdb=" O ALA A 452 " pdb=" OG SER A 455 " model vdw 2.268 2.440 nonbonded pdb=" OD2 ASP A 77 " pdb=" OG1 THR A 80 " model vdw 2.311 2.440 nonbonded pdb=" OH TYR A 168 " pdb=" OD1 ASN A 238 " model vdw 2.358 2.440 nonbonded pdb=" O MET A 52 " pdb=" OG1 THR A 56 " model vdw 2.363 2.440 ... (remaining 34087 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 2874 2.51 5 N 798 2.21 5 O 816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.330 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.040 Process input model: 16.230 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 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 : 0.008 0.063 4636 Z= 0.493 Angle : 1.101 9.311 6262 Z= 0.644 Chirality : 0.054 0.214 653 Planarity : 0.007 0.064 812 Dihedral : 10.299 50.156 1740 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.75 % 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: -4.98 (0.27), residues: 550 helix: -4.16 (0.15), residues: 249 sheet: -2.11 (0.73), residues: 51 loop : -2.47 (0.34), residues: 250 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 107 average time/residue: 0.2302 time to fit residues: 29.2567 Evaluate side-chains 58 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.580 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 124 GLN A 236 HIS A 276 HIS A 338 GLN A 347 GLN A 391 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4636 Z= 0.222 Angle : 0.671 7.521 6262 Z= 0.360 Chirality : 0.043 0.177 653 Planarity : 0.006 0.057 812 Dihedral : 6.364 35.291 626 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.45 % Favored : 92.36 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.10 (0.31), residues: 550 helix: -2.24 (0.25), residues: 257 sheet: -1.15 (0.98), residues: 29 loop : -1.87 (0.37), residues: 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.578 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 77 average time/residue: 0.1910 time to fit residues: 18.3471 Evaluate side-chains 58 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0453 time to fit residues: 1.2010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 17 optimal weight: 0.0970 chunk 40 optimal weight: 10.0000 overall best weight: 6.2188 ------------------------------------------------------------------------------- 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: 0.7328 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 4636 Z= 0.230 Angle : 0.637 6.185 6262 Z= 0.334 Chirality : 0.042 0.183 653 Planarity : 0.005 0.044 812 Dihedral : 5.986 34.815 626 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.34), residues: 550 helix: -1.27 (0.29), residues: 264 sheet: -0.86 (1.00), residues: 29 loop : -1.67 (0.40), residues: 257 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.564 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 62 average time/residue: 0.1719 time to fit residues: 13.8739 Evaluate side-chains 52 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.583 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0577 time to fit residues: 1.0704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 40.0000 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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: 0.7303 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 4636 Z= 0.180 Angle : 0.582 6.635 6262 Z= 0.303 Chirality : 0.041 0.155 653 Planarity : 0.004 0.038 812 Dihedral : 5.536 31.823 626 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.79 (0.35), residues: 550 helix: -0.84 (0.30), residues: 268 sheet: -0.40 (1.05), residues: 29 loop : -1.58 (0.41), residues: 253 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.554 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 61 average time/residue: 0.1615 time to fit residues: 13.0212 Evaluate side-chains 56 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.517 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0416 time to fit residues: 0.9274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 4636 Z= 0.260 Angle : 0.616 5.787 6262 Z= 0.322 Chirality : 0.042 0.151 653 Planarity : 0.004 0.035 812 Dihedral : 5.618 30.173 626 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.62 (0.35), residues: 550 helix: -0.61 (0.31), residues: 266 sheet: -0.45 (1.05), residues: 29 loop : -1.59 (0.40), residues: 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.594 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 0.1453 time to fit residues: 11.6052 Evaluate side-chains 55 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0590 time to fit residues: 1.1657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 30.0000 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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: 0.7328 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 4636 Z= 0.202 Angle : 0.587 6.947 6262 Z= 0.303 Chirality : 0.041 0.151 653 Planarity : 0.004 0.036 812 Dihedral : 5.409 29.752 626 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer Outliers : 1.04 % 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: -1.40 (0.36), residues: 550 helix: -0.43 (0.31), residues: 264 sheet: -0.37 (1.05), residues: 29 loop : -1.48 (0.40), residues: 257 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 57 average time/residue: 0.1546 time to fit residues: 11.8251 Evaluate side-chains 55 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.575 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0574 time to fit residues: 1.1558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 53 optimal weight: 0.0770 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- 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: 0.7317 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 4636 Z= 0.194 Angle : 0.585 5.756 6262 Z= 0.303 Chirality : 0.041 0.151 653 Planarity : 0.004 0.038 812 Dihedral : 5.286 29.729 626 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer Outliers : 0.62 % 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: -1.13 (0.36), residues: 550 helix: -0.19 (0.32), residues: 264 sheet: -0.15 (1.07), residues: 29 loop : -1.37 (0.40), residues: 257 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.567 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 57 average time/residue: 0.1582 time to fit residues: 12.0387 Evaluate side-chains 50 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.578 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0628 time to fit residues: 0.9846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.7325 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 4636 Z= 0.208 Angle : 0.610 8.412 6262 Z= 0.312 Chirality : 0.042 0.153 653 Planarity : 0.004 0.038 812 Dihedral : 5.271 28.937 626 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.36), residues: 550 helix: -0.17 (0.32), residues: 262 sheet: -0.06 (1.08), residues: 29 loop : -1.26 (0.41), residues: 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.500 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 0.1623 time to fit residues: 11.5135 Evaluate side-chains 51 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.569 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0429 time to fit residues: 0.8420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 4636 Z= 0.241 Angle : 0.627 7.698 6262 Z= 0.323 Chirality : 0.043 0.151 653 Planarity : 0.004 0.037 812 Dihedral : 5.417 29.496 626 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer Outliers : 0.00 % 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: -1.22 (0.36), residues: 550 helix: -0.32 (0.32), residues: 264 sheet: -0.03 (1.08), residues: 29 loop : -1.37 (0.40), residues: 257 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.576 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1492 time to fit residues: 10.4411 Evaluate side-chains 47 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.559 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- 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: 0.7314 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 4636 Z= 0.198 Angle : 0.617 7.358 6262 Z= 0.315 Chirality : 0.041 0.153 653 Planarity : 0.004 0.036 812 Dihedral : 5.281 28.986 626 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer Outliers : 0.00 % 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: -1.11 (0.37), residues: 550 helix: -0.25 (0.32), residues: 262 sheet: -0.08 (1.08), residues: 29 loop : -1.26 (0.41), residues: 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.705 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1556 time to fit residues: 11.3491 Evaluate side-chains 46 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.572 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.0040 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 0.0870 chunk 43 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 overall best weight: 3.2176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.072380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.064271 restraints weight = 18212.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.066007 restraints weight = 9844.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.067195 restraints weight = 6296.002| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 4636 Z= 0.183 Angle : 0.621 9.253 6262 Z= 0.318 Chirality : 0.041 0.168 653 Planarity : 0.004 0.036 812 Dihedral : 5.126 29.015 626 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer Outliers : 0.00 % 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: -1.03 (0.37), residues: 550 helix: -0.15 (0.32), residues: 263 sheet: -0.15 (1.03), residues: 29 loop : -1.25 (0.41), residues: 258 =============================================================================== Job complete usr+sys time: 1033.79 seconds wall clock time: 20 minutes 22.41 seconds (1222.41 seconds total)