Starting phenix.real_space_refine on Thu Dec 7 23:53:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugv_26497/12_2023/7ugv_26497_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugv_26497/12_2023/7ugv_26497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugv_26497/12_2023/7ugv_26497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugv_26497/12_2023/7ugv_26497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugv_26497/12_2023/7ugv_26497_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugv_26497/12_2023/7ugv_26497_updated.pdb" } resolution = 2.94 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= 0.036 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 2846 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 16 5.16 5 Na 3 4.78 5 C 2038 2.51 5 N 506 2.21 5 O 543 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 TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3107 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3107 Unusual residues: {' NA': 3} Inner-chain residues flagged as termini: ['pdbres="ASP A 501 "'] Classifications: {'peptide': 418, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 399, 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: 2.26, per 1000 atoms: 0.73 Number of scatterers: 3107 At special positions: 0 Unit cell: (69.012, 74.976, 74.124, 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 16 16.00 Na 3 11.00 F 1 9.00 O 543 8.00 N 506 7.00 C 2038 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: 1.39 Conformation dependent library (CDL) restraints added in 622.3 milliseconds 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 0 sheets defined 79.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 removed outlier: 3.505A pdb=" N TYR A 7 " --> pdb=" O LEU A 3 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 8 " --> pdb=" O TYR A 4 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3 through 9' Processing helix chain 'A' and resid 12 through 31 Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 44 through 70 removed outlier: 3.581A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N MET A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.604A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 80 through 107 removed outlier: 3.597A pdb=" N LYS A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.836A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 148 removed outlier: 3.661A pdb=" N LEU A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 170 removed outlier: 3.548A pdb=" N THR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 219 removed outlier: 3.504A pdb=" N LYS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.519A pdb=" N HIS A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 245 removed outlier: 3.569A pdb=" N GLY A 226 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 228 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A 236 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 237 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR A 240 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A 245 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 258 through 275 removed outlier: 5.203A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 291 Proline residue: A 283 - end of helix removed outlier: 3.517A pdb=" N ALA A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 299 No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 302 through 309 removed outlier: 4.173A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 329 removed outlier: 3.624A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.604A pdb=" N VAL A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 369 removed outlier: 3.523A pdb=" N MET A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N MET A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 416 removed outlier: 3.811A pdb=" N EFC A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 389 " --> pdb=" O EFC A 385 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 390 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 552 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: 0.82 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: 986 1.37 - 1.55: 2147 1.55 - 1.73: 1 1.73 - 1.92: 30 1.92 - 2.10: 1 Bond restraints: 3165 Sorted by residual: bond pdb=" N ILE A 309 " pdb=" CA ILE A 309 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 8.97e+00 bond pdb=" N LEU A 305 " pdb=" CA LEU A 305 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.20e+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 6.10e+00 bond pdb=" N LEU A 316 " pdb=" CA LEU A 316 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.72e+00 bond pdb=" N THR A 308 " pdb=" CA THR A 308 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.28e-02 6.10e+03 5.65e+00 ... (remaining 3160 not shown) Histogram of bond angle deviations from ideal: 100.48 - 106.63: 98 106.63 - 112.78: 1761 112.78 - 118.93: 805 118.93 - 125.08: 1618 125.08 - 131.23: 33 Bond angle restraints: 4315 Sorted by residual: angle pdb=" CA ILE A 309 " pdb=" C ILE A 309 " pdb=" O ILE A 309 " ideal model delta sigma weight residual 120.95 117.68 3.27 1.04e+00 9.25e-01 9.87e+00 angle pdb=" CB EFC A 385 " pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 101.65 110.23 -8.58 3.00e+00 1.11e-01 8.19e+00 angle pdb=" N LEU A 316 " pdb=" CA LEU A 316 " pdb=" C LEU A 316 " ideal model delta sigma weight residual 111.28 108.43 2.85 1.09e+00 8.42e-01 6.83e+00 angle pdb=" CA ALA A 307 " pdb=" C ALA A 307 " pdb=" O ALA A 307 " ideal model delta sigma weight residual 120.55 117.93 2.62 1.06e+00 8.90e-01 6.10e+00 angle pdb=" O GLY A 313 " pdb=" C GLY A 313 " pdb=" N THR A 314 " ideal model delta sigma weight residual 122.19 124.55 -2.36 9.60e-01 1.09e+00 6.04e+00 ... (remaining 4310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.18: 1773 15.18 - 30.36: 64 30.36 - 45.54: 11 45.54 - 60.73: 2 60.73 - 75.91: 3 Dihedral angle restraints: 1853 sinusoidal: 670 harmonic: 1183 Sorted by residual: dihedral pdb=" CB MET A 362 " pdb=" CG MET A 362 " pdb=" SD MET A 362 " pdb=" CE MET A 362 " ideal model delta sinusoidal sigma weight residual 60.00 102.25 -42.25 3 1.50e+01 4.44e-03 7.58e+00 dihedral pdb=" N LEU A 91 " pdb=" CA LEU A 91 " pdb=" CB LEU A 91 " pdb=" CG LEU A 91 " ideal model delta sinusoidal sigma weight residual -60.00 -94.69 34.69 3 1.50e+01 4.44e-03 5.89e+00 dihedral pdb=" N LEU A 78 " pdb=" CA LEU A 78 " pdb=" CB LEU A 78 " pdb=" CG LEU A 78 " ideal model delta sinusoidal sigma weight residual -180.00 -145.57 -34.43 3 1.50e+01 4.44e-03 5.83e+00 ... (remaining 1850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 368 0.034 - 0.068: 134 0.068 - 0.101: 29 0.101 - 0.135: 7 0.135 - 0.169: 2 Chirality restraints: 540 Sorted by residual: chirality pdb=" CA LEU A 305 " pdb=" N LEU A 305 " pdb=" C LEU A 305 " pdb=" CB LEU A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.14e-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 5.87e-01 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 2.65 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 537 not shown) Planarity restraints: 532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 376 " 0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO A 377 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 377 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 377 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 205 " -0.020 5.00e-02 4.00e+02 2.96e-02 1.41e+00 pdb=" N PRO A 206 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 10 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.23e+00 pdb=" N PRO A 11 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 11 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 11 " -0.015 5.00e-02 4.00e+02 ... (remaining 529 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 32 2.67 - 3.23: 3235 3.23 - 3.78: 4570 3.78 - 4.34: 6303 4.34 - 4.90: 10201 Nonbonded interactions: 24341 Sorted by model distance: nonbonded pdb=" O ASN A 310 " pdb="NA NA A 502 " model vdw 2.111 2.470 nonbonded pdb=" O THR A 308 " pdb="NA NA A 503 " model vdw 2.229 2.470 nonbonded pdb=" OD1 ASP A 312 " pdb="NA NA A 504 " model vdw 2.238 2.470 nonbonded pdb=" N GLY A 359 " pdb=" OD2 ASP A 501 " model vdw 2.377 2.520 nonbonded pdb=" O ALA A 348 " pdb=" OG1 THR A 352 " model vdw 2.389 2.440 ... (remaining 24336 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: 2.210 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: 8.990 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.910 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:14.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 3165 Z= 0.219 Angle : 0.566 8.583 4315 Z= 0.326 Chirality : 0.039 0.169 540 Planarity : 0.004 0.030 532 Dihedral : 9.131 75.906 1103 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 2.34 (0.40), residues: 412 helix: 1.83 (0.27), residues: 328 sheet: None (None), residues: 0 loop : 0.64 (0.76), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 219 PHE 0.006 0.001 PHE A 122 TYR 0.017 0.001 TYR A 89 ARG 0.001 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.375 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 1.3593 time to fit residues: 79.4964 Evaluate side-chains 38 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3165 Z= 0.183 Angle : 0.547 7.753 4315 Z= 0.281 Chirality : 0.038 0.123 540 Planarity : 0.005 0.031 532 Dihedral : 4.393 42.724 445 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.09 % Allowed : 9.26 % Favored : 87.65 % 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: 2.80 (0.41), residues: 412 helix: 2.09 (0.28), residues: 331 sheet: None (None), residues: 0 loop : 1.03 (0.75), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 32 PHE 0.011 0.001 PHE A 156 TYR 0.021 0.002 TYR A 89 ARG 0.005 0.001 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.325 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 42 average time/residue: 1.2695 time to fit residues: 54.9022 Evaluate side-chains 32 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 0.0857 time to fit residues: 0.5985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.0470 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 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: 0.8049 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3165 Z= 0.155 Angle : 0.491 7.886 4315 Z= 0.248 Chirality : 0.037 0.130 540 Planarity : 0.004 0.029 532 Dihedral : 4.085 36.759 445 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 3.40 % Allowed : 10.80 % Favored : 85.80 % 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: 3.04 (0.42), residues: 412 helix: 2.30 (0.29), residues: 330 sheet: None (None), residues: 0 loop : 0.96 (0.74), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 223 PHE 0.009 0.001 PHE A 50 TYR 0.013 0.001 TYR A 89 ARG 0.005 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 31 time to evaluate : 0.361 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 38 average time/residue: 1.2592 time to fit residues: 49.3435 Evaluate side-chains 30 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.5874 time to fit residues: 1.6864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.8081 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3165 Z= 0.195 Angle : 0.496 8.483 4315 Z= 0.248 Chirality : 0.037 0.140 540 Planarity : 0.004 0.029 532 Dihedral : 3.883 26.982 445 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.47 % Allowed : 12.35 % Favored : 85.19 % 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: 3.06 (0.42), residues: 412 helix: 2.27 (0.28), residues: 335 sheet: None (None), residues: 0 loop : 1.08 (0.78), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 368 PHE 0.009 0.001 PHE A 156 TYR 0.012 0.001 TYR A 383 ARG 0.005 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 30 time to evaluate : 0.313 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 36 average time/residue: 1.2886 time to fit residues: 47.8265 Evaluate side-chains 31 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 0.0783 time to fit residues: 0.5547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8091 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3165 Z= 0.194 Angle : 0.512 8.754 4315 Z= 0.251 Chirality : 0.037 0.148 540 Planarity : 0.004 0.030 532 Dihedral : 3.808 27.501 445 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.09 % Allowed : 12.96 % Favored : 83.95 % 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: 3.07 (0.42), residues: 412 helix: 2.31 (0.29), residues: 329 sheet: None (None), residues: 0 loop : 1.00 (0.74), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 368 PHE 0.009 0.001 PHE A 156 TYR 0.013 0.001 TYR A 383 ARG 0.006 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 31 time to evaluate : 0.360 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 38 average time/residue: 1.2953 time to fit residues: 50.7249 Evaluate side-chains 31 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.8095 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3165 Z= 0.206 Angle : 0.530 8.982 4315 Z= 0.261 Chirality : 0.038 0.191 540 Planarity : 0.004 0.031 532 Dihedral : 3.746 28.199 445 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 3.70 % Allowed : 13.89 % Favored : 82.41 % 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: 2.97 (0.42), residues: 412 helix: 2.35 (0.29), residues: 323 sheet: None (None), residues: 0 loop : 0.64 (0.72), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 368 PHE 0.016 0.001 PHE A 261 TYR 0.013 0.001 TYR A 383 ARG 0.006 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 28 time to evaluate : 0.359 Fit side-chains outliers start: 12 outliers final: 3 residues processed: 38 average time/residue: 1.2842 time to fit residues: 50.3081 Evaluate side-chains 32 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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: 0.8090 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3165 Z= 0.198 Angle : 0.529 9.248 4315 Z= 0.260 Chirality : 0.038 0.215 540 Planarity : 0.004 0.030 532 Dihedral : 3.715 27.619 445 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.47 % Allowed : 14.81 % Favored : 82.72 % 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: 3.03 (0.42), residues: 412 helix: 2.26 (0.28), residues: 329 sheet: None (None), residues: 0 loop : 1.10 (0.75), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 368 PHE 0.012 0.001 PHE A 261 TYR 0.012 0.001 TYR A 383 ARG 0.007 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 0.348 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 38 average time/residue: 1.2520 time to fit residues: 49.1051 Evaluate side-chains 33 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1633 time to fit residues: 0.6432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 0.0470 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.0670 chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 overall best weight: 0.3216 ------------------------------------------------------------------------------- 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: 0.8042 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3165 Z= 0.161 Angle : 0.543 9.465 4315 Z= 0.260 Chirality : 0.038 0.256 540 Planarity : 0.004 0.029 532 Dihedral : 3.673 26.129 445 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.47 % Allowed : 15.12 % Favored : 82.41 % 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: 3.07 (0.42), residues: 412 helix: 2.32 (0.29), residues: 327 sheet: None (None), residues: 0 loop : 1.04 (0.74), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.012 0.001 PHE A 261 TYR 0.009 0.001 TYR A 299 ARG 0.004 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.340 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 36 average time/residue: 1.3491 time to fit residues: 50.0231 Evaluate side-chains 33 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0030 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- 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: 0.8107 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3165 Z= 0.225 Angle : 0.552 9.368 4315 Z= 0.274 Chirality : 0.038 0.217 540 Planarity : 0.004 0.027 532 Dihedral : 3.632 24.338 445 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.16 % Allowed : 15.12 % Favored : 82.72 % 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: 2.87 (0.42), residues: 412 helix: 2.20 (0.29), residues: 329 sheet: None (None), residues: 0 loop : 0.82 (0.72), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 215 PHE 0.016 0.001 PHE A 261 TYR 0.014 0.001 TYR A 383 ARG 0.007 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.370 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 34 average time/residue: 1.3667 time to fit residues: 47.8905 Evaluate side-chains 32 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.320 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 0.0000 chunk 30 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3165 Z= 0.175 Angle : 0.551 9.276 4315 Z= 0.265 Chirality : 0.037 0.212 540 Planarity : 0.004 0.028 532 Dihedral : 3.626 24.012 445 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.62 % Allowed : 16.67 % Favored : 82.72 % 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: 2.94 (0.42), residues: 412 helix: 2.24 (0.28), residues: 329 sheet: None (None), residues: 0 loop : 0.88 (0.72), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 215 PHE 0.016 0.001 PHE A 261 TYR 0.009 0.001 TYR A 383 ARG 0.007 0.001 ARG A 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.333 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 32 average time/residue: 1.3722 time to fit residues: 45.2729 Evaluate side-chains 32 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.337 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.0030 chunk 38 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.0270 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.3448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.095381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.069555 restraints weight = 6117.881| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.58 r_work: 0.2801 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3165 Z= 0.163 Angle : 0.530 9.329 4315 Z= 0.258 Chirality : 0.037 0.189 540 Planarity : 0.004 0.028 532 Dihedral : 3.550 22.615 445 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.93 % Allowed : 16.36 % Favored : 82.72 % 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: 3.03 (0.42), residues: 412 helix: 2.30 (0.28), residues: 329 sheet: None (None), residues: 0 loop : 0.94 (0.73), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 368 PHE 0.016 0.001 PHE A 261 TYR 0.008 0.001 TYR A 299 ARG 0.007 0.001 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1569.83 seconds wall clock time: 28 minutes 26.79 seconds (1706.79 seconds total)