Starting phenix.real_space_refine on Sun Mar 10 16:23:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnc_9847/03_2024/6jnc_9847_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnc_9847/03_2024/6jnc_9847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnc_9847/03_2024/6jnc_9847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnc_9847/03_2024/6jnc_9847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnc_9847/03_2024/6jnc_9847_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnc_9847/03_2024/6jnc_9847_updated.pdb" } resolution = 3.7 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= 0.002 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2103 2.51 5 N 561 2.21 5 O 615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 78": "OE1" <-> "OE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 396": "NH1" <-> "NH2" 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: 3294 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3294 Unusual residues: {'TRS': 1} Inner-chain residues flagged as termini: ['pdbres="LYS A 419 "'] Classifications: {'peptide': 419, 'undetermined': 1} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 398, None: 1} Not linked: pdbres="LYS A 419 " pdbres="TRS A 901 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 2.33, per 1000 atoms: 0.71 Number of scatterers: 3294 At special positions: 0 Unit cell: (71.34, 75.69, 74.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 615 8.00 N 561 7.00 C 2103 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: 1.12 Conformation dependent library (CDL) restraints added in 733.0 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 4 sheets defined 41.8% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 6 through 18 removed outlier: 3.611A pdb=" N GLN A 13 " --> pdb=" O MET A 9 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 28 No H-bonds generated for 'chain 'A' and resid 25 through 28' Processing helix chain 'A' and resid 81 through 90 removed outlier: 3.902A pdb=" N LEU A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.834A pdb=" N ILE A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 152 through 164 removed outlier: 3.617A pdb=" N MET A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 190 through 206 removed outlier: 3.982A pdb=" N ALA A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.530A pdb=" N THR A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 266 removed outlier: 4.105A pdb=" N LEU A 261 " --> pdb=" O PRO A 257 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.961A pdb=" N ASP A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 343 No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.542A pdb=" N SER A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 391 removed outlier: 3.534A pdb=" N LYS A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A 376 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN A 386 " --> pdb=" O TRP A 382 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP A 390 " --> pdb=" O ASN A 386 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 391 " --> pdb=" O THR A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 413 removed outlier: 3.575A pdb=" N TYR A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 36 through 45 removed outlier: 3.521A pdb=" N ARG A 36 " --> pdb=" O GLN A 60 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLY A 104 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 75 removed outlier: 6.654A pdb=" N GLY A 106 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N HIS A 75 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ILE A 108 " --> pdb=" O HIS A 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 291 through 294 removed outlier: 6.493A pdb=" N THR A 238 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL A 217 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL A 240 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 removed outlier: 6.716A pdb=" N LEU A 336 " --> pdb=" O VAL A 314 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 92 hydrogen bonds defined for protein. 273 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: 0.81 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1061 1.34 - 1.45: 435 1.45 - 1.57: 1841 1.57 - 1.69: 0 1.69 - 1.80: 29 Bond restraints: 3366 Sorted by residual: bond pdb=" CA PHE A 341 " pdb=" C PHE A 341 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.48e-02 4.57e+03 1.45e+01 bond pdb=" N TRS A 901 " pdb=" C TRS A 901 " ideal model delta sigma weight residual 1.501 1.462 0.039 2.00e-02 2.50e+03 3.79e+00 bond pdb=" CB VAL A 356 " pdb=" CG2 VAL A 356 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.59e+00 bond pdb=" CB TRP A 382 " pdb=" CG TRP A 382 " ideal model delta sigma weight residual 1.498 1.449 0.049 3.10e-02 1.04e+03 2.49e+00 bond pdb=" C PHE A 341 " pdb=" N LEU A 342 " ideal model delta sigma weight residual 1.335 1.315 0.020 1.42e-02 4.96e+03 1.96e+00 ... (remaining 3361 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.08: 88 106.08 - 113.13: 1844 113.13 - 120.17: 1228 120.17 - 127.21: 1352 127.21 - 134.25: 50 Bond angle restraints: 4562 Sorted by residual: angle pdb=" N ILE A 181 " pdb=" CA ILE A 181 " pdb=" C ILE A 181 " ideal model delta sigma weight residual 113.20 107.26 5.94 9.60e-01 1.09e+00 3.83e+01 angle pdb=" C ASP A 340 " pdb=" N PHE A 341 " pdb=" CA PHE A 341 " ideal model delta sigma weight residual 122.65 114.88 7.77 1.60e+00 3.91e-01 2.36e+01 angle pdb=" N VAL A 97 " pdb=" CA VAL A 97 " pdb=" C VAL A 97 " ideal model delta sigma weight residual 112.17 108.44 3.73 9.50e-01 1.11e+00 1.54e+01 angle pdb=" C LYS A 271 " pdb=" N ASP A 272 " pdb=" CA ASP A 272 " ideal model delta sigma weight residual 122.19 127.16 -4.97 1.41e+00 5.03e-01 1.24e+01 angle pdb=" C VAL A 146 " pdb=" N TYR A 147 " pdb=" CA TYR A 147 " ideal model delta sigma weight residual 123.05 128.57 -5.52 1.57e+00 4.06e-01 1.24e+01 ... (remaining 4557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 1792 16.63 - 33.27: 164 33.27 - 49.90: 47 49.90 - 66.53: 11 66.53 - 83.17: 2 Dihedral angle restraints: 2016 sinusoidal: 818 harmonic: 1198 Sorted by residual: dihedral pdb=" CA TRP A 382 " pdb=" C TRP A 382 " pdb=" N GLU A 383 " pdb=" CA GLU A 383 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ASP A 290 " pdb=" CB ASP A 290 " pdb=" CG ASP A 290 " pdb=" OD1 ASP A 290 " ideal model delta sinusoidal sigma weight residual -30.00 -90.08 60.08 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA TYR A 147 " pdb=" C TYR A 147 " pdb=" N THR A 148 " pdb=" CA THR A 148 " ideal model delta harmonic sigma weight residual 180.00 163.58 16.42 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 2013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 259 0.035 - 0.070: 161 0.070 - 0.105: 48 0.105 - 0.139: 22 0.139 - 0.174: 7 Chirality restraints: 497 Sorted by residual: chirality pdb=" CB ILE A 23 " pdb=" CA ILE A 23 " pdb=" CG1 ILE A 23 " pdb=" CG2 ILE A 23 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CA PHE A 341 " pdb=" N PHE A 341 " pdb=" C PHE A 341 " pdb=" CB PHE A 341 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA TYR A 147 " pdb=" N TYR A 147 " pdb=" C TYR A 147 " pdb=" CB TYR A 147 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 494 not shown) Planarity restraints: 584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 149 " 0.044 5.00e-02 4.00e+02 6.53e-02 6.83e+00 pdb=" N PRO A 150 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO A 142 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 99 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.83e+00 pdb=" N PRO A 100 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 100 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 100 " 0.033 5.00e-02 4.00e+02 ... (remaining 581 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1079 2.82 - 3.34: 2659 3.34 - 3.86: 5082 3.86 - 4.38: 6004 4.38 - 4.90: 10445 Nonbonded interactions: 25269 Sorted by model distance: nonbonded pdb=" N ASP A 340 " pdb=" OD1 ASP A 340 " model vdw 2.304 2.520 nonbonded pdb=" OD2 ASP A 145 " pdb=" O2 TRS A 901 " model vdw 2.368 2.440 nonbonded pdb=" N ASP A 256 " pdb=" OD1 ASP A 256 " model vdw 2.370 2.520 nonbonded pdb=" O PHE A 353 " pdb=" NE2 GLN A 357 " model vdw 2.372 2.520 nonbonded pdb=" N ASN A 149 " pdb=" OD1 ASN A 149 " model vdw 2.377 2.520 ... (remaining 25264 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.360 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.950 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.009 0.062 3366 Z= 0.541 Angle : 0.872 7.773 4562 Z= 0.560 Chirality : 0.052 0.174 497 Planarity : 0.008 0.065 584 Dihedral : 14.724 83.169 1252 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 9.09 % Allowed : 10.85 % Favored : 80.06 % 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: -5.69 (0.30), residues: 417 helix: -4.85 (0.13), residues: 188 sheet: -1.75 (0.68), residues: 61 loop : -2.99 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 30 HIS 0.006 0.001 HIS A 388 PHE 0.011 0.002 PHE A 57 TYR 0.012 0.002 TYR A 363 ARG 0.003 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 83 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 5 ASP cc_start: 0.7896 (t70) cc_final: 0.7309 (t0) REVERT: A 48 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7689 (p0) REVERT: A 180 SER cc_start: 0.8179 (p) cc_final: 0.7593 (m) REVERT: A 246 ARG cc_start: 0.6032 (OUTLIER) cc_final: 0.5805 (ttt90) REVERT: A 269 SER cc_start: 0.7051 (t) cc_final: 0.6632 (p) outliers start: 31 outliers final: 5 residues processed: 105 average time/residue: 0.1826 time to fit residues: 22.6312 Evaluate side-chains 59 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 348 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 386 ASN A 394 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3366 Z= 0.221 Angle : 0.566 5.548 4562 Z= 0.304 Chirality : 0.046 0.139 497 Planarity : 0.006 0.043 584 Dihedral : 7.004 55.226 474 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 6.16 % Allowed : 14.66 % Favored : 79.18 % 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: -3.93 (0.34), residues: 417 helix: -3.11 (0.27), residues: 184 sheet: -1.50 (0.66), residues: 57 loop : -2.20 (0.42), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 263 HIS 0.002 0.001 HIS A 267 PHE 0.011 0.002 PHE A 273 TYR 0.031 0.002 TYR A 225 ARG 0.002 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 55 time to evaluate : 0.383 Fit side-chains REVERT: A 5 ASP cc_start: 0.7804 (t70) cc_final: 0.7320 (t0) REVERT: A 69 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8444 (ttmt) REVERT: A 180 SER cc_start: 0.8383 (p) cc_final: 0.8016 (m) REVERT: A 246 ARG cc_start: 0.6355 (OUTLIER) cc_final: 0.5534 (ttt90) REVERT: A 249 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7653 (mm) REVERT: A 269 SER cc_start: 0.7629 (t) cc_final: 0.7132 (p) REVERT: A 331 ARG cc_start: 0.7503 (tmm-80) cc_final: 0.7149 (ptm-80) outliers start: 21 outliers final: 7 residues processed: 71 average time/residue: 0.1573 time to fit residues: 13.6880 Evaluate side-chains 56 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 400 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3366 Z= 0.187 Angle : 0.475 3.948 4562 Z= 0.256 Chirality : 0.044 0.134 497 Planarity : 0.004 0.038 584 Dihedral : 6.326 44.540 473 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.40 % Allowed : 18.18 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.37), residues: 417 helix: -1.98 (0.34), residues: 188 sheet: -1.15 (0.67), residues: 57 loop : -2.06 (0.43), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 89 HIS 0.003 0.001 HIS A 388 PHE 0.009 0.001 PHE A 341 TYR 0.025 0.001 TYR A 225 ARG 0.004 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8546 (ttmt) REVERT: A 145 ASP cc_start: 0.7579 (t0) cc_final: 0.7363 (t70) REVERT: A 246 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.5680 (ttt90) REVERT: A 249 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7631 (mm) REVERT: A 331 ARG cc_start: 0.7628 (tmm-80) cc_final: 0.7280 (ptm160) outliers start: 15 outliers final: 9 residues processed: 54 average time/residue: 0.1857 time to fit residues: 12.2169 Evaluate side-chains 51 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 365 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 10.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3366 Z= 0.147 Angle : 0.444 3.828 4562 Z= 0.231 Chirality : 0.044 0.134 497 Planarity : 0.004 0.032 584 Dihedral : 5.840 41.867 473 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.11 % Allowed : 19.94 % Favored : 75.95 % 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: -2.54 (0.38), residues: 417 helix: -1.49 (0.36), residues: 189 sheet: -1.04 (0.68), residues: 57 loop : -1.99 (0.43), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.004 0.001 HIS A 388 PHE 0.006 0.001 PHE A 341 TYR 0.023 0.001 TYR A 225 ARG 0.003 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 0.402 Fit side-chains REVERT: A 69 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8558 (ttmt) REVERT: A 145 ASP cc_start: 0.7553 (t0) cc_final: 0.7348 (t70) REVERT: A 246 ARG cc_start: 0.6346 (OUTLIER) cc_final: 0.5708 (ttt90) REVERT: A 249 ILE cc_start: 0.7899 (pt) cc_final: 0.7540 (mm) outliers start: 14 outliers final: 8 residues processed: 52 average time/residue: 0.1496 time to fit residues: 9.8861 Evaluate side-chains 49 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.6742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3366 Z= 0.234 Angle : 0.506 5.575 4562 Z= 0.263 Chirality : 0.046 0.145 497 Planarity : 0.004 0.030 584 Dihedral : 5.973 41.599 471 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.11 % Allowed : 20.53 % Favored : 75.37 % 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: -2.14 (0.40), residues: 417 helix: -1.21 (0.37), residues: 189 sheet: -0.39 (0.67), residues: 67 loop : -1.98 (0.45), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 89 HIS 0.004 0.001 HIS A 388 PHE 0.011 0.001 PHE A 341 TYR 0.015 0.001 TYR A 225 ARG 0.004 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8554 (ttmt) REVERT: A 237 MET cc_start: 0.5213 (OUTLIER) cc_final: 0.4752 (ttm) REVERT: A 284 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8304 (tp) outliers start: 14 outliers final: 11 residues processed: 50 average time/residue: 0.1378 time to fit residues: 8.9020 Evaluate side-chains 50 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 36 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.0050 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.7145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3366 Z= 0.206 Angle : 0.478 5.492 4562 Z= 0.246 Chirality : 0.045 0.154 497 Planarity : 0.003 0.029 584 Dihedral : 5.438 41.725 465 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.40 % Allowed : 19.94 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.40), residues: 417 helix: -0.89 (0.38), residues: 190 sheet: -0.25 (0.68), residues: 67 loop : -1.87 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 89 HIS 0.003 0.001 HIS A 388 PHE 0.007 0.001 PHE A 341 TYR 0.028 0.001 TYR A 225 ARG 0.001 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 37 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8571 (ttmt) outliers start: 15 outliers final: 10 residues processed: 47 average time/residue: 0.1355 time to fit residues: 8.2618 Evaluate side-chains 46 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 35 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.7418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3366 Z= 0.276 Angle : 0.507 5.384 4562 Z= 0.262 Chirality : 0.046 0.160 497 Planarity : 0.004 0.029 584 Dihedral : 5.724 44.344 465 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.40 % Allowed : 19.35 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.41), residues: 417 helix: -0.80 (0.38), residues: 190 sheet: -0.31 (0.67), residues: 67 loop : -1.89 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 30 HIS 0.004 0.001 HIS A 388 PHE 0.010 0.001 PHE A 341 TYR 0.016 0.001 TYR A 225 ARG 0.002 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 34 time to evaluate : 0.398 Fit side-chains REVERT: A 69 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8621 (ttmt) REVERT: A 218 GLN cc_start: 0.8381 (tt0) cc_final: 0.8039 (tp40) REVERT: A 249 ILE cc_start: 0.8020 (tp) cc_final: 0.7654 (mm) REVERT: A 262 LYS cc_start: 0.8059 (tmtt) cc_final: 0.7697 (mtmt) REVERT: A 265 ARG cc_start: 0.7821 (mtt180) cc_final: 0.7548 (mmm-85) outliers start: 15 outliers final: 12 residues processed: 46 average time/residue: 0.1388 time to fit residues: 8.3380 Evaluate side-chains 44 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 31 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 388 HIS Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.7502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3366 Z= 0.160 Angle : 0.448 5.787 4562 Z= 0.232 Chirality : 0.044 0.141 497 Planarity : 0.003 0.028 584 Dihedral : 5.362 43.652 465 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.11 % Allowed : 19.35 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.41), residues: 417 helix: -0.49 (0.39), residues: 190 sheet: -0.13 (0.66), residues: 67 loop : -1.79 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 92 HIS 0.003 0.001 HIS A 388 PHE 0.006 0.001 PHE A 341 TYR 0.019 0.001 TYR A 225 ARG 0.001 0.000 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 33 time to evaluate : 0.337 Fit side-chains REVERT: A 69 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8600 (ttmt) REVERT: A 218 GLN cc_start: 0.8369 (tt0) cc_final: 0.8111 (tp40) REVERT: A 249 ILE cc_start: 0.8042 (tp) cc_final: 0.7732 (mm) REVERT: A 262 LYS cc_start: 0.8067 (tmtt) cc_final: 0.7713 (mtmt) REVERT: A 265 ARG cc_start: 0.7748 (mtt180) cc_final: 0.7477 (mmm-85) outliers start: 14 outliers final: 11 residues processed: 43 average time/residue: 0.1354 time to fit residues: 7.5377 Evaluate side-chains 43 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 31 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 24 optimal weight: 30.0000 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 0.0870 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 overall best weight: 1.3760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.7576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3366 Z= 0.146 Angle : 0.443 5.872 4562 Z= 0.227 Chirality : 0.044 0.145 497 Planarity : 0.003 0.029 584 Dihedral : 5.185 45.680 465 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.52 % Allowed : 20.53 % Favored : 75.95 % 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: -1.15 (0.42), residues: 417 helix: -0.22 (0.39), residues: 190 sheet: 0.08 (0.68), residues: 67 loop : -1.70 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 92 HIS 0.002 0.001 HIS A 388 PHE 0.005 0.001 PHE A 57 TYR 0.032 0.001 TYR A 225 ARG 0.001 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 33 time to evaluate : 0.394 Fit side-chains REVERT: A 69 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8582 (ttmt) REVERT: A 218 GLN cc_start: 0.8366 (tt0) cc_final: 0.8076 (tp40) REVERT: A 249 ILE cc_start: 0.8058 (tp) cc_final: 0.7759 (mm) REVERT: A 262 LYS cc_start: 0.8082 (tmtt) cc_final: 0.7730 (mtmt) REVERT: A 265 ARG cc_start: 0.7733 (mtt180) cc_final: 0.7278 (mmm-85) outliers start: 12 outliers final: 10 residues processed: 42 average time/residue: 0.1458 time to fit residues: 7.9431 Evaluate side-chains 42 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 31 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 393 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.7666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3366 Z= 0.140 Angle : 0.458 6.095 4562 Z= 0.235 Chirality : 0.044 0.137 497 Planarity : 0.003 0.028 584 Dihedral : 5.109 46.354 465 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.52 % Allowed : 20.23 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.42), residues: 417 helix: -0.01 (0.40), residues: 190 sheet: 0.32 (0.70), residues: 67 loop : -1.58 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 92 HIS 0.004 0.001 HIS A 267 PHE 0.005 0.001 PHE A 341 TYR 0.028 0.001 TYR A 225 ARG 0.001 0.000 ARG A 265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 31 time to evaluate : 0.352 Fit side-chains REVERT: A 69 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8567 (ttmt) REVERT: A 218 GLN cc_start: 0.8387 (tt0) cc_final: 0.8116 (tp40) REVERT: A 249 ILE cc_start: 0.8073 (tp) cc_final: 0.7776 (mm) REVERT: A 262 LYS cc_start: 0.8398 (tmtt) cc_final: 0.8153 (ttmt) REVERT: A 266 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6587 (mm-30) REVERT: A 303 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7617 (pt0) outliers start: 12 outliers final: 10 residues processed: 41 average time/residue: 0.1461 time to fit residues: 7.7531 Evaluate side-chains 43 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 31 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 393 ILE 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: 3.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 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 = 0.3293 r_free = 0.3293 target = 0.114499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.092053 restraints weight = 5096.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.090903 restraints weight = 6650.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.091320 restraints weight = 6448.249| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.7702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3366 Z= 0.215 Angle : 0.488 6.033 4562 Z= 0.250 Chirality : 0.045 0.133 497 Planarity : 0.003 0.029 584 Dihedral : 5.418 48.427 465 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.40 % Allowed : 19.65 % Favored : 75.95 % 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: -0.94 (0.42), residues: 417 helix: -0.07 (0.39), residues: 190 sheet: 0.27 (0.70), residues: 67 loop : -1.62 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 355 HIS 0.004 0.001 HIS A 388 PHE 0.008 0.001 PHE A 341 TYR 0.026 0.001 TYR A 225 ARG 0.001 0.000 ARG A 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 979.43 seconds wall clock time: 18 minutes 19.27 seconds (1099.27 seconds total)