Starting phenix.real_space_refine on Fri Dec 8 00:03:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh6_26505/12_2023/7uh6_26505_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh6_26505/12_2023/7uh6_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_26505/12_2023/7uh6_26505.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh6_26505/12_2023/7uh6_26505.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh6_26505/12_2023/7uh6_26505_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh6_26505/12_2023/7uh6_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-1.21rc1-5172/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: 2.22, per 1000 atoms: 0.72 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: 1.38 Conformation dependent library (CDL) restraints added in 578.5 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: 0.67 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: 0.84 Time building geometry restraints manager: 1.47 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: 2.670 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: 11.320 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.100 Find NCS groups from input model: 0.130 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.290 ------------------------------------------------------------------------------- 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 : 0.342 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.1067 time to fit residues: 6.1182 Evaluate side-chains 32 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4546 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.8980 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7839 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3153 Z= 0.173 Angle : 0.609 10.056 4298 Z= 0.296 Chirality : 0.038 0.144 538 Planarity : 0.004 0.028 529 Dihedral : 3.992 19.994 443 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.24 % Allowed : 8.67 % Favored : 90.09 % 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: 1.68 (0.41), residues: 410 helix: 1.41 (0.28), residues: 321 sheet: None (None), residues: 0 loop : 0.29 (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 45 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.363 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.1088 time to fit residues: 6.1505 Evaluate side-chains 37 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0372 time to fit residues: 0.6006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.0060 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 37 optimal weight: 0.0170 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 overall best weight: 0.3034 ------------------------------------------------------------------------------- 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: 0.7797 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3153 Z= 0.149 Angle : 0.583 9.335 4298 Z= 0.278 Chirality : 0.038 0.177 538 Planarity : 0.004 0.030 529 Dihedral : 3.807 19.370 443 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.93 % Allowed : 9.91 % Favored : 89.16 % 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: 1.54 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 0.17 (0.75), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 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 45 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.312 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.1090 time to fit residues: 6.3829 Evaluate side-chains 38 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.320 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0475 time to fit residues: 0.4819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7816 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3153 Z= 0.148 Angle : 0.595 12.710 4298 Z= 0.275 Chirality : 0.038 0.142 538 Planarity : 0.003 0.031 529 Dihedral : 3.792 17.439 443 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.24 % Allowed : 11.15 % Favored : 87.62 % 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: 1.86 (0.42), residues: 410 helix: 1.58 (0.29), residues: 322 sheet: None (None), residues: 0 loop : 0.13 (0.74), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 264 PHE 0.010 0.001 PHE A 261 TYR 0.019 0.001 TYR A 88 ARG 0.001 0.000 ARG A 395 *********************** 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 48 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.350 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.1272 time to fit residues: 7.2731 Evaluate side-chains 41 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0344 time to fit residues: 0.6324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.0670 chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 0.0470 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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: 0.7800 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 0.022 3153 Z= 0.143 Angle : 0.589 10.931 4298 Z= 0.276 Chirality : 0.038 0.140 538 Planarity : 0.003 0.031 529 Dihedral : 3.767 17.374 443 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 13.31 % Favored : 86.69 % 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 (0.43), residues: 410 helix: 1.63 (0.29), residues: 322 sheet: None (None), residues: 0 loop : 0.08 (0.74), residues: 88 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 0.006 0.001 TYR A 383 ARG 0.001 0.000 ARG A 397 *********************** 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 40 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.309 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1007 time to fit residues: 5.5767 Evaluate side-chains 39 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.302 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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: 0.7815 moved from start: 0.3382 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= 0.155 Angle : 0.610 9.371 4298 Z= 0.282 Chirality : 0.038 0.145 538 Planarity : 0.003 0.031 529 Dihedral : 3.756 17.381 443 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.24 % Allowed : 14.86 % Favored : 83.90 % 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: 1.81 (0.43), residues: 410 helix: 1.55 (0.29), residues: 323 sheet: None (None), residues: 0 loop : 0.07 (0.74), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 114 PHE 0.010 0.001 PHE A 261 TYR 0.006 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: 4 poor density : 41 time to evaluate : 0.345 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 44 average time/residue: 0.1019 time to fit residues: 6.1621 Evaluate side-chains 40 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0356 time to fit residues: 0.5247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 25 optimal weight: 0.0770 overall best weight: 0.8940 ------------------------------------------------------------------------------- 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: 0.7835 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3153 Z= 0.165 Angle : 0.607 9.150 4298 Z= 0.288 Chirality : 0.038 0.135 538 Planarity : 0.003 0.032 529 Dihedral : 3.785 17.465 443 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 16.72 % Favored : 83.28 % 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: 1.80 (0.43), residues: 410 helix: 1.53 (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 0.004 0.001 HIS A 114 PHE 0.010 0.001 PHE A 261 TYR 0.007 0.001 TYR A 383 ARG 0.002 0.000 ARG A 395 *********************** 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 39 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.373 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1062 time to fit residues: 5.8425 Evaluate side-chains 39 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.325 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.0570 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- 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: 0.7896 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3153 Z= 0.227 Angle : 0.653 9.076 4298 Z= 0.312 Chirality : 0.039 0.147 538 Planarity : 0.004 0.031 529 Dihedral : 3.975 17.847 443 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.62 % Allowed : 16.72 % Favored : 82.66 % 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: 1.61 (0.43), residues: 410 helix: 1.40 (0.29), residues: 322 sheet: None (None), residues: 0 loop : 0.06 (0.75), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 264 PHE 0.010 0.001 PHE A 261 TYR 0.009 0.001 TYR A 383 ARG 0.003 0.000 ARG A 395 *********************** 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 39 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.331 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 37 average time/residue: 0.1028 time to fit residues: 5.3196 Evaluate side-chains 38 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.326 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0358 time to fit residues: 0.5608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.7858 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3153 Z= 0.179 Angle : 0.651 9.469 4298 Z= 0.307 Chirality : 0.039 0.148 538 Planarity : 0.003 0.031 529 Dihedral : 3.944 17.774 443 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 17.96 % 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: 1.60 (0.43), residues: 410 helix: 1.45 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -0.18 (0.74), residues: 89 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 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 39 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.375 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1061 time to fit residues: 5.7705 Evaluate side-chains 36 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.362 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.0030 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- 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: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3153 Z= 0.170 Angle : 0.655 10.442 4298 Z= 0.313 Chirality : 0.039 0.147 538 Planarity : 0.004 0.031 529 Dihedral : 3.916 17.582 443 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.62 % Allowed : 18.89 % Favored : 80.50 % 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: 1.68 (0.43), residues: 410 helix: 1.50 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -0.16 (0.74), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 264 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 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 39 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.314 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 37 average time/residue: 0.1052 time to fit residues: 5.3395 Evaluate side-chains 38 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.324 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0430 time to fit residues: 0.5837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.0040 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.084751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.070668 restraints weight = 13843.253| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.97 r_work: 0.3240 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3153 Z= 0.170 Angle : 0.680 10.216 4298 Z= 0.322 Chirality : 0.041 0.276 538 Planarity : 0.003 0.031 529 Dihedral : 3.856 17.509 443 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 19.81 % Favored : 80.19 % 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: 1.50 (0.43), residues: 410 helix: 1.37 (0.29), residues: 323 sheet: None (None), residues: 0 loop : -0.23 (0.74), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 264 PHE 0.011 0.001 PHE A 261 TYR 0.007 0.001 TYR A 383 ARG 0.001 0.000 ARG A 395 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1130.93 seconds wall clock time: 21 minutes 1.76 seconds (1261.76 seconds total)