Starting phenix.real_space_refine on Sun Mar 10 23:14:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugv_26497/03_2024/7ugv_26497_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugv_26497/03_2024/7ugv_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_26497/03_2024/7ugv_26497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugv_26497/03_2024/7ugv_26497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugv_26497/03_2024/7ugv_26497_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugv_26497/03_2024/7ugv_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-dev-5265/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: 2.17, per 1000 atoms: 0.70 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: 1.35 Conformation dependent library (CDL) restraints added in 619.9 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: 0.63 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: 0.80 Time building geometry restraints manager: 1.46 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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 8.820 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.620 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:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.590 ------------------------------------------------------------------------------- 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 : 0.341 Fit side-chains REVERT: A 5 ARG cc_start: 0.7830 (mmt90) cc_final: 0.7573 (mmt-90) REVERT: A 121 GLN cc_start: 0.9068 (mt0) cc_final: 0.8747 (mt0) REVERT: A 291 GLU cc_start: 0.8584 (mp0) cc_final: 0.8340 (mp0) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 1.2818 time to fit residues: 75.0042 Evaluate side-chains 40 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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: 0.8980 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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: 0.8089 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3165 Z= 0.194 Angle : 0.544 7.723 4315 Z= 0.280 Chirality : 0.038 0.122 540 Planarity : 0.004 0.031 532 Dihedral : 4.339 44.443 445 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.78 % Allowed : 9.26 % Favored : 87.96 % 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: 2.86 (0.41), residues: 412 helix: 2.15 (0.28), residues: 331 sheet: None (None), residues: 0 loop : 0.99 (0.75), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 32 PHE 0.009 0.001 PHE A 156 TYR 0.020 0.002 TYR A 89 ARG 0.004 0.001 ARG A 80 *********************** 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 45 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.346 Fit side-chains REVERT: A 5 ARG cc_start: 0.7896 (mmt90) cc_final: 0.7662 (mmt-90) REVERT: A 9 GLU cc_start: 0.8463 (mp0) cc_final: 0.8182 (pm20) REVERT: A 120 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8416 (tp-100) REVERT: A 125 HIS cc_start: 0.8686 (OUTLIER) cc_final: 0.8435 (t-90) REVERT: A 291 GLU cc_start: 0.8695 (mp0) cc_final: 0.8448 (mp0) outliers start: 9 outliers final: 4 residues processed: 44 average time/residue: 1.3847 time to fit residues: 62.5853 Evaluate side-chains 37 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 0.0270 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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: 0.8075 moved from start: 0.2466 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= 0.177 Angle : 0.502 8.108 4315 Z= 0.252 Chirality : 0.037 0.130 540 Planarity : 0.004 0.028 532 Dihedral : 4.108 38.032 445 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.40 % Allowed : 11.11 % Favored : 85.49 % 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: 3.00 (0.42), residues: 412 helix: 2.26 (0.28), residues: 330 sheet: None (None), residues: 0 loop : 1.00 (0.76), 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 0.014 0.001 TYR A 89 ARG 0.004 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 43 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 0.372 Fit side-chains REVERT: A 5 ARG cc_start: 0.7965 (mmt90) cc_final: 0.7704 (mmt-90) REVERT: A 9 GLU cc_start: 0.8502 (mp0) cc_final: 0.8248 (pm20) REVERT: A 125 HIS cc_start: 0.8687 (OUTLIER) cc_final: 0.8452 (t-90) REVERT: A 150 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7106 (mt0) REVERT: A 291 GLU cc_start: 0.8721 (mp0) cc_final: 0.8398 (mp0) outliers start: 11 outliers final: 4 residues processed: 41 average time/residue: 1.3645 time to fit residues: 57.5264 Evaluate side-chains 36 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 369 SER 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: 0.8980 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.8112 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3165 Z= 0.233 Angle : 0.506 8.129 4315 Z= 0.256 Chirality : 0.038 0.148 540 Planarity : 0.004 0.028 532 Dihedral : 3.920 28.343 445 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 2.95 (0.42), residues: 412 helix: 2.23 (0.28), residues: 330 sheet: None (None), residues: 0 loop : 0.98 (0.76), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 368 PHE 0.011 0.001 PHE A 50 TYR 0.015 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 42 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.325 Fit side-chains REVERT: A 5 ARG cc_start: 0.7992 (mmt90) cc_final: 0.7705 (mmt-90) REVERT: A 9 GLU cc_start: 0.8487 (mp0) cc_final: 0.8197 (pm20) REVERT: A 120 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8360 (tp-100) REVERT: A 150 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7173 (mt0) REVERT: A 291 GLU cc_start: 0.8739 (mp0) cc_final: 0.8357 (mp0) outliers start: 10 outliers final: 5 residues processed: 40 average time/residue: 1.4431 time to fit residues: 59.2605 Evaluate side-chains 37 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 369 SER 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: 0.3980 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2739 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= 0.190 Angle : 0.503 8.794 4315 Z= 0.248 Chirality : 0.037 0.143 540 Planarity : 0.004 0.028 532 Dihedral : 3.816 28.384 445 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.55 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: 3.06 (0.42), residues: 412 helix: 2.31 (0.29), residues: 329 sheet: None (None), residues: 0 loop : 0.97 (0.76), 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 42 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.340 Fit side-chains REVERT: A 5 ARG cc_start: 0.7959 (mmt90) cc_final: 0.6797 (mmt-90) REVERT: A 9 GLU cc_start: 0.8485 (mp0) cc_final: 0.7768 (mp0) REVERT: A 150 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7202 (mt0) REVERT: A 291 GLU cc_start: 0.8775 (mp0) cc_final: 0.8461 (mp0) outliers start: 10 outliers final: 3 residues processed: 40 average time/residue: 1.4581 time to fit residues: 59.8336 Evaluate side-chains 33 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 369 SER 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: 0.9980 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8094 moved from start: 0.2870 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= 0.184 Angle : 0.519 8.982 4315 Z= 0.253 Chirality : 0.037 0.153 540 Planarity : 0.004 0.030 532 Dihedral : 3.740 28.879 445 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 3.70 % Allowed : 13.27 % Favored : 83.02 % 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: 2.31 (0.29), residues: 329 sheet: None (None), residues: 0 loop : 0.96 (0.75), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 215 PHE 0.009 0.001 PHE A 156 TYR 0.012 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 45 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 33 time to evaluate : 0.344 Fit side-chains REVERT: A 5 ARG cc_start: 0.7995 (mmt90) cc_final: 0.6995 (mtt-85) REVERT: A 9 GLU cc_start: 0.8491 (mp0) cc_final: 0.7738 (mp0) REVERT: A 150 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7245 (mt0) REVERT: A 291 GLU cc_start: 0.8787 (mp0) cc_final: 0.8452 (mp0) outliers start: 12 outliers final: 6 residues processed: 43 average time/residue: 1.3894 time to fit residues: 61.3447 Evaluate side-chains 37 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 374 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8097 moved from start: 0.2938 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= 0.191 Angle : 0.526 9.243 4315 Z= 0.256 Chirality : 0.037 0.158 540 Planarity : 0.004 0.031 532 Dihedral : 3.679 27.485 445 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 3.70 % Allowed : 13.58 % 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: 3.04 (0.42), residues: 412 helix: 2.33 (0.29), residues: 327 sheet: None (None), residues: 0 loop : 0.89 (0.74), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 368 PHE 0.015 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 44 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 32 time to evaluate : 0.355 Fit side-chains REVERT: A 5 ARG cc_start: 0.7973 (mmt90) cc_final: 0.6951 (mtt-85) REVERT: A 9 GLU cc_start: 0.8474 (mp0) cc_final: 0.7694 (mp0) REVERT: A 150 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7223 (mt0) REVERT: A 291 GLU cc_start: 0.8760 (mp0) cc_final: 0.8414 (mp0) outliers start: 12 outliers final: 4 residues processed: 40 average time/residue: 1.4574 time to fit residues: 59.8943 Evaluate side-chains 37 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 369 SER 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: 1.9990 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.0470 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 0.0010 chunk 34 optimal weight: 0.9980 overall best weight: 0.7486 ------------------------------------------------------------------------------- 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: 0.3039 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= 0.189 Angle : 0.542 9.541 4315 Z= 0.260 Chirality : 0.037 0.162 540 Planarity : 0.004 0.031 532 Dihedral : 3.647 26.301 445 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.78 % Allowed : 14.51 % 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: 3.00 (0.42), residues: 412 helix: 2.35 (0.29), residues: 327 sheet: None (None), residues: 0 loop : 0.62 (0.72), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 215 PHE 0.013 0.001 PHE A 261 TYR 0.012 0.001 TYR A 383 ARG 0.007 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 41 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.354 Fit side-chains REVERT: A 5 ARG cc_start: 0.7987 (mmt90) cc_final: 0.6979 (mtt-85) REVERT: A 9 GLU cc_start: 0.8450 (mp0) cc_final: 0.7649 (mp0) REVERT: A 150 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7226 (mt0) REVERT: A 291 GLU cc_start: 0.8769 (mp0) cc_final: 0.8412 (mp0) outliers start: 9 outliers final: 4 residues processed: 39 average time/residue: 1.3511 time to fit residues: 54.2174 Evaluate side-chains 37 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 369 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.0570 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 38 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3165 Z= 0.166 Angle : 0.526 9.410 4315 Z= 0.254 Chirality : 0.037 0.156 540 Planarity : 0.004 0.028 532 Dihedral : 3.600 25.038 445 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.09 % Allowed : 13.89 % Favored : 83.02 % 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: 3.05 (0.42), residues: 412 helix: 2.37 (0.29), residues: 327 sheet: None (None), residues: 0 loop : 0.71 (0.73), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 215 PHE 0.017 0.001 PHE A 261 TYR 0.009 0.001 TYR A 299 ARG 0.005 0.001 ARG A 80 *********************** 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 44 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 34 time to evaluate : 0.310 Fit side-chains REVERT: A 5 ARG cc_start: 0.7994 (mmt90) cc_final: 0.6975 (mtt-85) REVERT: A 9 GLU cc_start: 0.8447 (mp0) cc_final: 0.7638 (mp0) REVERT: A 150 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7182 (mt0) REVERT: A 287 ARG cc_start: 0.9090 (tmm-80) cc_final: 0.8794 (tmm-80) REVERT: A 291 GLU cc_start: 0.8794 (mp0) cc_final: 0.8427 (mp0) outliers start: 10 outliers final: 4 residues processed: 42 average time/residue: 1.4062 time to fit residues: 60.5932 Evaluate side-chains 37 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 369 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.3980 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 0.0030 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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: 0.8077 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3165 Z= 0.184 Angle : 0.541 8.916 4315 Z= 0.264 Chirality : 0.038 0.247 540 Planarity : 0.004 0.027 532 Dihedral : 3.535 23.382 445 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.54 % Allowed : 15.43 % Favored : 83.02 % 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: 2.95 (0.42), residues: 412 helix: 2.26 (0.29), residues: 328 sheet: None (None), residues: 0 loop : 0.84 (0.74), residues: 84 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 0.010 0.001 TYR A 383 ARG 0.004 0.000 ARG A 80 ********************** 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 41 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.361 Fit side-chains REVERT: A 5 ARG cc_start: 0.8027 (mmt90) cc_final: 0.7041 (mtt-85) REVERT: A 9 GLU cc_start: 0.8440 (mp0) cc_final: 0.7618 (mp0) REVERT: A 150 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7198 (mt0) REVERT: A 257 ASP cc_start: 0.8476 (t0) cc_final: 0.8153 (OUTLIER) REVERT: A 287 ARG cc_start: 0.9105 (tmm-80) cc_final: 0.8812 (tmm-80) REVERT: A 291 GLU cc_start: 0.8799 (mp0) cc_final: 0.8432 (mp0) outliers start: 5 outliers final: 4 residues processed: 40 average time/residue: 1.4736 time to fit residues: 60.5031 Evaluate side-chains 41 residues out of total 324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 369 SER 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: 0.8980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.092855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.066440 restraints weight = 6085.252| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.62 r_work: 0.2740 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3204 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= 0.208 Angle : 0.553 8.973 4315 Z= 0.270 Chirality : 0.039 0.272 540 Planarity : 0.004 0.028 532 Dihedral : 3.527 22.369 445 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.23 % Allowed : 15.12 % Favored : 83.64 % 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: 2.20 (0.29), residues: 328 sheet: None (None), residues: 0 loop : 1.10 (0.74), residues: 84 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 0.012 0.001 TYR A 383 ARG 0.004 0.000 ARG A 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1632.56 seconds wall clock time: 29 minutes 41.66 seconds (1781.66 seconds total)