Starting phenix.real_space_refine on Sun Mar 10 23:22:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh6_26505/03_2024/7uh6_26505_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh6_26505/03_2024/7uh6_26505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh6_26505/03_2024/7uh6_26505.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh6_26505/03_2024/7uh6_26505.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh6_26505/03_2024/7uh6_26505_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh6_26505/03_2024/7uh6_26505_updated.pdb" } resolution = 3.44 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= 0.003 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2933 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians S 17 5.16 5 Na 3 4.78 5 C 2032 2.51 5 N 504 2.21 5 O 538 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 172": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 501": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3095 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3095 Unusual residues: {' NA': 3} Inner-chain residues flagged as termini: ['pdbres="ASP A 501 "'] Classifications: {'peptide': 416, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 397, None: 3} Not linked: pdbres="ASP A 501 " pdbres=" NA A 502 " Not linked: pdbres=" NA A 502 " pdbres=" NA A 503 " Not linked: pdbres=" NA A 503 " pdbres=" NA A 504 " Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EFC:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.18, per 1000 atoms: 0.70 Number of scatterers: 3095 At special positions: 0 Unit cell: (74.124, 76.68, 70.716, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 17 16.00 Na 3 11.00 F 1 9.00 O 538 8.00 N 504 7.00 C 2032 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: 1.30 Conformation dependent library (CDL) restraints added in 580.1 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 0 sheets defined 78.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 removed outlier: 3.592A pdb=" N LYS A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 33 removed outlier: 3.543A pdb=" N LEU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 42 Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 58 through 72 Processing helix chain 'A' and resid 81 through 107 removed outlier: 3.543A pdb=" N TYR A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 142 through 148 removed outlier: 4.086A pdb=" N LEU A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 169 removed outlier: 3.919A pdb=" N TYR A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 220 removed outlier: 3.524A pdb=" N LYS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 199 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.547A pdb=" N HIS A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 245 removed outlier: 3.828A pdb=" N VAL A 231 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A 235 " --> pdb=" O THR A 232 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 236 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 241 " --> pdb=" O GLY A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 253 removed outlier: 3.734A pdb=" N LEU A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 275 removed outlier: 3.613A pdb=" N LYS A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 291 Proline residue: A 283 - end of helix removed outlier: 3.759A pdb=" N VAL A 288 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 290 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 309 removed outlier: 3.631A pdb=" N PHE A 301 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR A 302 " --> pdb=" O TYR A 299 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU A 303 " --> pdb=" O SER A 300 " (cutoff:3.500A) Proline residue: A 304 - end of helix removed outlier: 3.618A pdb=" N ALA A 307 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 308 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE A 309 " --> pdb=" O GLY A 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 309' Processing helix chain 'A' and resid 312 through 329 removed outlier: 3.511A pdb=" N ALA A 326 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.620A pdb=" N THR A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 4.305A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N MET A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 387 removed outlier: 3.672A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 414 removed outlier: 4.157A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 398 " --> pdb=" O ASP A 394 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N MET A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) 190 hydrogen bonds defined for protein. 507 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: 0.79 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 980 1.37 - 1.55: 2140 1.55 - 1.73: 0 1.73 - 1.92: 32 1.92 - 2.10: 1 Bond restraints: 3153 Sorted by residual: bond pdb=" N ILE A 309 " pdb=" CA ILE A 309 " ideal model delta sigma weight residual 1.461 1.495 -0.033 1.17e-02 7.31e+03 8.12e+00 bond pdb=" N VAL A 320 " pdb=" CA VAL A 320 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.44e+00 bond pdb=" N THR A 281 " pdb=" CA THR A 281 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 6.80e+00 bond pdb=" N ASN A 310 " pdb=" CA ASN A 310 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.23e-02 6.61e+03 6.08e+00 bond pdb=" N ASP A 312 " pdb=" CA ASP A 312 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 5.95e+00 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 100.28 - 106.47: 96 106.47 - 112.66: 1735 112.66 - 118.86: 810 118.86 - 125.05: 1626 125.05 - 131.24: 31 Bond angle restraints: 4298 Sorted by residual: angle pdb=" CA MET A 311 " pdb=" C MET A 311 " pdb=" O MET A 311 " ideal model delta sigma weight residual 121.67 118.00 3.67 9.30e-01 1.16e+00 1.55e+01 angle pdb=" CA ILE A 309 " pdb=" C ILE A 309 " pdb=" O ILE A 309 " ideal model delta sigma weight residual 121.17 117.88 3.29 1.06e+00 8.90e-01 9.66e+00 angle pdb=" N THR A 281 " pdb=" CA THR A 281 " pdb=" C THR A 281 " ideal model delta sigma weight residual 112.93 109.65 3.28 1.12e+00 7.97e-01 8.57e+00 angle pdb=" CA GLY A 319 " pdb=" C GLY A 319 " pdb=" O GLY A 319 " ideal model delta sigma weight residual 121.00 118.14 2.86 1.08e+00 8.57e-01 7.03e+00 angle pdb=" O VAL A 320 " pdb=" C VAL A 320 " pdb=" N ALA A 321 " ideal model delta sigma weight residual 121.87 124.42 -2.55 9.70e-01 1.06e+00 6.93e+00 ... (remaining 4293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.54: 1657 11.54 - 23.07: 121 23.07 - 34.61: 55 34.61 - 46.14: 12 46.14 - 57.68: 3 Dihedral angle restraints: 1848 sinusoidal: 669 harmonic: 1179 Sorted by residual: dihedral pdb=" CB MET A 59 " pdb=" CG MET A 59 " pdb=" SD MET A 59 " pdb=" CE MET A 59 " ideal model delta sinusoidal sigma weight residual -180.00 -122.32 -57.68 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CG ARG A 395 " pdb=" CD ARG A 395 " pdb=" NE ARG A 395 " pdb=" CZ ARG A 395 " ideal model delta sinusoidal sigma weight residual 180.00 138.77 41.23 2 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CA GLU A 291 " pdb=" C GLU A 291 " pdb=" N MET A 292 " pdb=" CA MET A 292 " ideal model delta harmonic sigma weight residual 180.00 164.87 15.13 0 5.00e+00 4.00e-02 9.15e+00 ... (remaining 1845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 390 0.040 - 0.080: 114 0.080 - 0.120: 28 0.120 - 0.159: 5 0.159 - 0.199: 1 Chirality restraints: 538 Sorted by residual: chirality pdb=" CA MET A 311 " pdb=" N MET A 311 " pdb=" C MET A 311 " pdb=" CB MET A 311 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CA LEU A 316 " pdb=" N LEU A 316 " pdb=" C LEU A 316 " pdb=" CB LEU A 316 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE A 309 " pdb=" N ILE A 309 " pdb=" C ILE A 309 " pdb=" CB ILE A 309 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 535 not shown) Planarity restraints: 529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 108 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C ASN A 108 " -0.025 2.00e-02 2.50e+03 pdb=" O ASN A 108 " 0.009 2.00e-02 2.50e+03 pdb=" N PRO A 109 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 301 " -0.009 2.00e-02 2.50e+03 1.09e-02 2.06e+00 pdb=" CG PHE A 301 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 301 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 301 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 301 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 301 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 301 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 89 " 0.011 2.00e-02 2.50e+03 8.85e-03 1.57e+00 pdb=" CG TYR A 89 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 89 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 89 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 89 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 89 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 89 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 89 " 0.001 2.00e-02 2.50e+03 ... (remaining 526 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 18 2.59 - 3.17: 2849 3.17 - 3.74: 4849 3.74 - 4.32: 6234 4.32 - 4.90: 9914 Nonbonded interactions: 23864 Sorted by model distance: nonbonded pdb=" OD1 ASP A 312 " pdb="NA NA A 504 " model vdw 2.012 2.470 nonbonded pdb=" O SER A 349 " pdb="NA NA A 503 " model vdw 2.145 2.470 nonbonded pdb=" OH TYR A 236 " pdb=" O ILE A 392 " model vdw 2.263 2.440 nonbonded pdb=" O LEU A 282 " pdb=" OG1 THR A 285 " model vdw 2.291 2.440 nonbonded pdb=" O VAL A 412 " pdb=" OG1 THR A 415 " model vdw 2.338 2.440 ... (remaining 23859 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: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 11.500 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 13.710 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3153 Z= 0.214 Angle : 0.633 7.760 4298 Z= 0.363 Chirality : 0.041 0.199 538 Planarity : 0.003 0.026 529 Dihedral : 10.580 57.677 1100 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.31 % Allowed : 0.31 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.39), residues: 410 helix: 0.86 (0.28), residues: 314 sheet: None (None), residues: 0 loop : -0.13 (0.64), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.025 0.001 PHE A 301 TYR 0.021 0.001 TYR A 89 ARG 0.001 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.261 Fit side-chains REVERT: A 1 MET cc_start: 0.5669 (ptt) cc_final: 0.5321 (ptp) REVERT: A 310 ASN cc_start: 0.6600 (t0) cc_final: 0.6168 (t0) REVERT: A 343 LEU cc_start: 0.9136 (tt) cc_final: 0.8815 (mt) outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.1051 time to fit residues: 6.0128 Evaluate side-chains 32 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7840 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3153 Z= 0.172 Angle : 0.614 10.357 4298 Z= 0.297 Chirality : 0.038 0.141 538 Planarity : 0.004 0.029 529 Dihedral : 4.043 20.219 443 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.24 % Allowed : 8.98 % Favored : 89.78 % 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: 1.65 (0.41), residues: 410 helix: 1.39 (0.28), residues: 321 sheet: None (None), residues: 0 loop : 0.28 (0.73), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 264 PHE 0.016 0.001 PHE A 323 TYR 0.013 0.001 TYR A 88 ARG 0.002 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5670 (ptt) cc_final: 0.5316 (ptp) REVERT: A 311 MET cc_start: 0.7849 (tpp) cc_final: 0.7486 (mmt) REVERT: A 343 LEU cc_start: 0.9029 (tt) cc_final: 0.8732 (mt) REVERT: A 362 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7100 (ttt) outliers start: 4 outliers final: 2 residues processed: 42 average time/residue: 0.1054 time to fit residues: 6.0420 Evaluate side-chains 39 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.0470 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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: 0.7804 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3153 Z= 0.146 Angle : 0.576 9.515 4298 Z= 0.273 Chirality : 0.038 0.137 538 Planarity : 0.004 0.030 529 Dihedral : 3.766 19.212 443 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.86 % Allowed : 10.84 % Favored : 87.31 % 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: 1.83 (0.42), residues: 410 helix: 1.55 (0.29), residues: 323 sheet: None (None), residues: 0 loop : 0.14 (0.75), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 264 PHE 0.011 0.001 PHE A 323 TYR 0.009 0.001 TYR A 299 ARG 0.002 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.329 Fit side-chains REVERT: A 1 MET cc_start: 0.5638 (ptt) cc_final: 0.5276 (ptp) REVERT: A 134 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9018 (mm) REVERT: A 311 MET cc_start: 0.7795 (tpp) cc_final: 0.7407 (mmt) REVERT: A 343 LEU cc_start: 0.9026 (tt) cc_final: 0.8705 (mt) REVERT: A 362 MET cc_start: 0.7621 (ttp) cc_final: 0.7055 (ttt) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 0.1032 time to fit residues: 5.9850 Evaluate side-chains 43 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 406 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 9.9990 chunk 28 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 35 optimal weight: 0.0570 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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: 0.7784 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3153 Z= 0.139 Angle : 0.571 9.598 4298 Z= 0.270 Chirality : 0.038 0.144 538 Planarity : 0.003 0.031 529 Dihedral : 3.750 17.372 443 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.55 % Allowed : 12.07 % Favored : 86.38 % 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: 1.91 (0.42), residues: 410 helix: 1.63 (0.29), residues: 323 sheet: None (None), residues: 0 loop : 0.06 (0.74), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 264 PHE 0.010 0.001 PHE A 261 TYR 0.006 0.001 TYR A 383 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.387 Fit side-chains REVERT: A 1 MET cc_start: 0.5575 (ptt) cc_final: 0.5215 (ptp) REVERT: A 134 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9048 (mm) REVERT: A 311 MET cc_start: 0.7907 (tpp) cc_final: 0.7532 (mmt) outliers start: 5 outliers final: 2 residues processed: 45 average time/residue: 0.1278 time to fit residues: 7.4558 Evaluate side-chains 40 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 406 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.0060 chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 0.0770 chunk 7 optimal weight: 8.9990 overall best weight: 0.8156 ------------------------------------------------------------------------------- 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: 0.7819 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3153 Z= 0.159 Angle : 0.615 13.017 4298 Z= 0.283 Chirality : 0.040 0.273 538 Planarity : 0.003 0.031 529 Dihedral : 3.764 17.272 443 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.93 % Allowed : 14.86 % Favored : 84.21 % 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: 1.89 (0.43), residues: 410 helix: 1.60 (0.29), residues: 324 sheet: None (None), residues: 0 loop : 0.08 (0.76), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 114 PHE 0.010 0.001 PHE A 261 TYR 0.007 0.001 TYR A 383 ARG 0.001 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.376 Fit side-chains REVERT: A 1 MET cc_start: 0.5630 (ptt) cc_final: 0.5269 (ptp) REVERT: A 134 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9061 (mm) REVERT: A 311 MET cc_start: 0.8003 (tpp) cc_final: 0.7703 (mmt) outliers start: 3 outliers final: 2 residues processed: 43 average time/residue: 0.1069 time to fit residues: 6.2977 Evaluate side-chains 40 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 406 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7823 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3153 Z= 0.156 Angle : 0.631 11.093 4298 Z= 0.287 Chirality : 0.040 0.318 538 Planarity : 0.003 0.031 529 Dihedral : 3.759 17.380 443 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.17 % Allowed : 14.86 % Favored : 82.97 % 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: 1.75 (0.43), residues: 410 helix: 1.51 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -0.00 (0.75), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 114 PHE 0.009 0.001 PHE A 261 TYR 0.007 0.001 TYR A 383 ARG 0.001 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.324 Fit side-chains REVERT: A 1 MET cc_start: 0.5652 (ptt) cc_final: 0.5271 (ptp) REVERT: A 134 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9079 (mm) REVERT: A 311 MET cc_start: 0.8052 (tpp) cc_final: 0.7796 (mmt) outliers start: 7 outliers final: 3 residues processed: 41 average time/residue: 0.1003 time to fit residues: 5.6793 Evaluate side-chains 42 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 406 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 25 optimal weight: 0.2980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.7845 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3153 Z= 0.172 Angle : 0.646 10.449 4298 Z= 0.298 Chirality : 0.040 0.309 538 Planarity : 0.003 0.031 529 Dihedral : 3.809 17.485 443 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.24 % Allowed : 16.72 % Favored : 82.04 % 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: 1.76 (0.43), residues: 410 helix: 1.51 (0.30), residues: 316 sheet: None (None), residues: 0 loop : 0.20 (0.73), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 114 PHE 0.009 0.001 PHE A 261 TYR 0.007 0.001 TYR A 383 ARG 0.001 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.339 Fit side-chains REVERT: A 1 MET cc_start: 0.5686 (ptt) cc_final: 0.5301 (ptp) REVERT: A 134 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9086 (mm) REVERT: A 311 MET cc_start: 0.8037 (tpp) cc_final: 0.7816 (mmt) outliers start: 4 outliers final: 2 residues processed: 40 average time/residue: 0.1001 time to fit residues: 5.5428 Evaluate side-chains 41 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 406 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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: 0.7917 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3153 Z= 0.240 Angle : 0.657 8.971 4298 Z= 0.317 Chirality : 0.042 0.288 538 Planarity : 0.004 0.031 529 Dihedral : 4.001 17.729 443 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.93 % Allowed : 17.65 % Favored : 81.42 % 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: 1.56 (0.43), residues: 410 helix: 1.39 (0.30), residues: 315 sheet: None (None), residues: 0 loop : 0.05 (0.72), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 264 PHE 0.010 0.001 PHE A 261 TYR 0.009 0.001 TYR A 383 ARG 0.002 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.350 Fit side-chains REVERT: A 1 MET cc_start: 0.5729 (ptt) cc_final: 0.5351 (ptp) REVERT: A 134 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9148 (mm) REVERT: A 362 MET cc_start: 0.8246 (mtp) cc_final: 0.7944 (mtp) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.1054 time to fit residues: 5.2773 Evaluate side-chains 38 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 406 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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: 0.7877 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3153 Z= 0.188 Angle : 0.649 9.344 4298 Z= 0.304 Chirality : 0.041 0.298 538 Planarity : 0.003 0.031 529 Dihedral : 3.913 18.253 443 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.24 % Allowed : 17.65 % Favored : 81.11 % 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: 1.55 (0.43), residues: 410 helix: 1.39 (0.30), residues: 315 sheet: None (None), residues: 0 loop : 0.02 (0.72), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 114 PHE 0.009 0.001 PHE A 261 TYR 0.008 0.001 TYR A 383 ARG 0.001 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.366 Fit side-chains REVERT: A 1 MET cc_start: 0.5714 (ptt) cc_final: 0.5329 (ptp) REVERT: A 134 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9131 (mm) REVERT: A 362 MET cc_start: 0.8200 (mtp) cc_final: 0.7958 (mtp) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.1172 time to fit residues: 5.9875 Evaluate side-chains 39 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 406 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7836 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3153 Z= 0.159 Angle : 0.650 10.074 4298 Z= 0.301 Chirality : 0.040 0.317 538 Planarity : 0.004 0.031 529 Dihedral : 3.812 18.885 443 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.24 % Allowed : 17.34 % Favored : 81.42 % 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: 1.51 (0.43), residues: 410 helix: 1.39 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -0.27 (0.74), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 114 PHE 0.009 0.001 PHE A 261 TYR 0.026 0.001 TYR A 299 ARG 0.002 0.000 ARG A 397 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.324 Fit side-chains REVERT: A 1 MET cc_start: 0.5643 (ptt) cc_final: 0.5255 (ptp) REVERT: A 134 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9155 (mm) REVERT: A 227 GLU cc_start: 0.8494 (mp0) cc_final: 0.8256 (mp0) REVERT: A 362 MET cc_start: 0.8165 (mtp) cc_final: 0.7924 (mtp) outliers start: 4 outliers final: 2 residues processed: 39 average time/residue: 0.1083 time to fit residues: 5.7982 Evaluate side-chains 38 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 406 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.0020 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.085204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.071448 restraints weight = 13732.134| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.94 r_work: 0.3269 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3153 Z= 0.162 Angle : 0.662 10.535 4298 Z= 0.312 Chirality : 0.041 0.320 538 Planarity : 0.003 0.031 529 Dihedral : 3.812 18.846 443 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.93 % Allowed : 18.27 % Favored : 80.80 % 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: 1.39 (0.43), residues: 410 helix: 1.27 (0.29), residues: 324 sheet: None (None), residues: 0 loop : -0.15 (0.74), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 114 PHE 0.009 0.001 PHE A 261 TYR 0.024 0.001 TYR A 299 ARG 0.001 0.000 ARG A 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1202.83 seconds wall clock time: 22 minutes 38.31 seconds (1358.31 seconds total)