Starting phenix.real_space_refine on Thu Mar 13 14:20:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eo4_19845/03_2025/9eo4_19845_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eo4_19845/03_2025/9eo4_19845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eo4_19845/03_2025/9eo4_19845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eo4_19845/03_2025/9eo4_19845.map" model { file = "/net/cci-nas-00/data/ceres_data/9eo4_19845/03_2025/9eo4_19845_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eo4_19845/03_2025/9eo4_19845_neut_trim.cif" } resolution = 2.66 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= -0.001 sd= 0.034 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: 7 Type Number sf(0) Gaussians S 23 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 3001 2.51 5 N 685 2.21 5 O 748 1.98 5 H 4322 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8781 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 8634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 8634 Classifications: {'peptide': 546} Modifications used: {'ACID-ASP': 1, 'ACID-GLU': 1} Link IDs: {'PTRANS': 23, 'TRANS': 522} Chain breaks: 1 Chain: "B" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 147 Unusual residues: {' CL': 1, ' NA': 1, 'CLR': 3, 'COC': 1, 'Y01': 1} Classifications: {'undetermined': 7, 'water': 4} Link IDs: {None: 10} Time building chain proxies: 5.95, per 1000 atoms: 0.68 Number of scatterers: 8781 At special positions: 0 Unit cell: (83.375, 66.7, 80.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 23 16.00 Na 1 11.00 O 748 8.00 N 685 7.00 C 3001 6.00 H 4322 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 189 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.92 Conformation dependent library (CDL) restraints added in 639.1 milliseconds 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 1 sheets defined 82.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'B' and resid 65 through 78 removed outlier: 3.904A pdb=" N PHE B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 85 Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 109 through 125 removed outlier: 3.543A pdb=" N LEU B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 138 Processing helix chain 'B' and resid 139 through 153 removed outlier: 3.800A pdb=" N PHE B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 169 removed outlier: 3.684A pdb=" N ILE B 159 " --> pdb=" O PHE B 155 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 160 " --> pdb=" O TYR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 220 Processing helix chain 'B' and resid 223 through 227 removed outlier: 3.538A pdb=" N GLN B 226 " --> pdb=" O HIS B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 256 Processing helix chain 'B' and resid 258 through 270 removed outlier: 4.445A pdb=" N LYS B 264 " --> pdb=" O LYS B 260 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TRP B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 286 removed outlier: 4.033A pdb=" N THR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.588A pdb=" N CYS B 306 " --> pdb=" O TYR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 322 removed outlier: 3.834A pdb=" N TRP B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 334 Processing helix chain 'B' and resid 341 through 376 removed outlier: 3.693A pdb=" N GLY B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE B 362 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL B 363 " --> pdb=" O SER B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 383 Processing helix chain 'B' and resid 388 through 400 removed outlier: 3.708A pdb=" N ILE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR B 394 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Proline residue: B 395 - end of helix removed outlier: 3.805A pdb=" N THR B 400 " --> pdb=" O GLU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 438 removed outlier: 3.772A pdb=" N ASP B 421 " --> pdb=" O THR B 417 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 442 Processing helix chain 'B' and resid 444 through 460 removed outlier: 3.605A pdb=" N PHE B 448 " --> pdb=" O HIS B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 467 through 479 removed outlier: 3.801A pdb=" N VAL B 471 " --> pdb=" O GLY B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 497 removed outlier: 3.614A pdb=" N LEU B 485 " --> pdb=" O GLY B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 513 Processing helix chain 'B' and resid 517 through 526 Processing helix chain 'B' and resid 526 through 542 Processing helix chain 'B' and resid 554 through 570 removed outlier: 3.835A pdb=" N SER B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 583 Processing helix chain 'B' and resid 586 through 596 removed outlier: 3.561A pdb=" N LEU B 591 " --> pdb=" O PHE B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 599 No H-bonds generated for 'chain 'B' and resid 597 through 599' Processing helix chain 'B' and resid 600 through 607 Processing helix chain 'B' and resid 609 through 612 Processing helix chain 'B' and resid 613 through 619 removed outlier: 3.648A pdb=" N TRP B 617 " --> pdb=" O THR B 613 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 547 through 548 removed outlier: 3.639A pdb=" N TYR B 548 " --> pdb=" O TYR B 551 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 822 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: 3.50 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4312 1.03 - 1.23: 45 1.23 - 1.43: 1925 1.43 - 1.62: 2606 1.62 - 1.82: 34 Bond restraints: 8922 Sorted by residual: bond pdb=" N ALA B 57 " pdb=" H ALA B 57 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C LYS B 66 " pdb=" O LYS B 66 " ideal model delta sigma weight residual 1.236 1.172 0.064 1.29e-02 6.01e+03 2.43e+01 bond pdb=" C29 COC B 707 " pdb=" C8 COC B 707 " ideal model delta sigma weight residual 1.528 1.615 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C SER B 586 " pdb=" O SER B 586 " ideal model delta sigma weight residual 1.234 1.189 0.045 1.07e-02 8.73e+03 1.80e+01 bond pdb=" C SER B 568 " pdb=" O SER B 568 " ideal model delta sigma weight residual 1.236 1.188 0.049 1.16e-02 7.43e+03 1.78e+01 ... (remaining 8917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 15923 2.47 - 4.94: 121 4.94 - 7.41: 9 7.41 - 9.88: 2 9.88 - 12.34: 2 Bond angle restraints: 16057 Sorted by residual: angle pdb=" CA SER B 568 " pdb=" C SER B 568 " pdb=" O SER B 568 " ideal model delta sigma weight residual 120.90 115.19 5.71 1.03e+00 9.43e-01 3.07e+01 angle pdb=" N SER B 568 " pdb=" CA SER B 568 " pdb=" C SER B 568 " ideal model delta sigma weight residual 111.03 105.21 5.82 1.11e+00 8.12e-01 2.75e+01 angle pdb=" CA SER B 586 " pdb=" C SER B 586 " pdb=" O SER B 586 " ideal model delta sigma weight residual 121.67 116.04 5.63 1.26e+00 6.30e-01 2.00e+01 angle pdb=" CA MET B 569 " pdb=" C MET B 569 " pdb=" O MET B 569 " ideal model delta sigma weight residual 120.10 115.18 4.92 1.13e+00 7.83e-01 1.90e+01 angle pdb=" N ARG B 588 " pdb=" CA ARG B 588 " pdb=" C ARG B 588 " ideal model delta sigma weight residual 112.90 107.33 5.57 1.31e+00 5.83e-01 1.81e+01 ... (remaining 16052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 4279 35.73 - 71.46: 164 71.46 - 107.19: 8 107.19 - 142.92: 1 142.92 - 178.64: 2 Dihedral angle restraints: 4454 sinusoidal: 2433 harmonic: 2021 Sorted by residual: dihedral pdb=" CD ARG B 443 " pdb=" NE ARG B 443 " pdb=" CZ ARG B 443 " pdb=" NH1 ARG B 443 " ideal model delta sinusoidal sigma weight residual 0.00 -78.07 78.07 1 1.00e+01 1.00e-02 7.62e+01 dihedral pdb=" CB ASP B 421 " pdb=" CG ASP B 421 " pdb=" OD2 ASP B 421 " pdb=" HD2 ASP B 421 " ideal model delta harmonic sigma weight residual -180.00 -1.36 -178.64 0 3.00e+01 1.11e-03 3.55e+01 dihedral pdb=" CG GLU B 491 " pdb=" CD GLU B 491 " pdb=" OE2 GLU B 491 " pdb=" HE2 GLU B 491 " ideal model delta harmonic sigma weight residual 180.00 1.54 178.46 0 3.00e+01 1.11e-03 3.54e+01 ... (remaining 4451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 616 0.057 - 0.113: 96 0.113 - 0.170: 8 0.170 - 0.226: 0 0.226 - 0.283: 2 Chirality restraints: 722 Sorted by residual: chirality pdb=" C8 COC B 707 " pdb=" C10 COC B 707 " pdb=" C29 COC B 707 " pdb=" C6 COC B 707 " both_signs ideal model delta sigma weight residual False 2.53 2.81 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C29 COC B 707 " pdb=" C26 COC B 707 " pdb=" C8 COC B 707 " pdb=" O1 COC B 707 " both_signs ideal model delta sigma weight residual False -2.38 -2.64 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ILE B 67 " pdb=" N ILE B 67 " pdb=" C ILE B 67 " pdb=" CB ILE B 67 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 719 not shown) Planarity restraints: 1271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 443 " 1.080 9.50e-02 1.11e+02 5.49e-01 3.98e+03 pdb=" NE ARG B 443 " -0.081 2.00e-02 2.50e+03 pdb=" CZ ARG B 443 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG B 443 " 0.059 2.00e-02 2.50e+03 pdb=" NH2 ARG B 443 " -0.056 2.00e-02 2.50e+03 pdb="HH11 ARG B 443 " 0.729 2.00e-02 2.50e+03 pdb="HH12 ARG B 443 " -0.540 2.00e-02 2.50e+03 pdb="HH21 ARG B 443 " 0.529 2.00e-02 2.50e+03 pdb="HH22 ARG B 443 " -0.651 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 85 " -0.271 9.50e-02 1.11e+02 4.20e-01 3.79e+03 pdb=" NE ARG B 85 " 0.326 2.00e-02 2.50e+03 pdb=" CZ ARG B 85 " 0.087 2.00e-02 2.50e+03 pdb=" NH1 ARG B 85 " -0.058 2.00e-02 2.50e+03 pdb=" NH2 ARG B 85 " -0.019 2.00e-02 2.50e+03 pdb="HH11 ARG B 85 " 0.632 2.00e-02 2.50e+03 pdb="HH12 ARG B 85 " -0.842 2.00e-02 2.50e+03 pdb="HH21 ARG B 85 " -0.429 2.00e-02 2.50e+03 pdb="HH22 ARG B 85 " 0.316 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 317 " 0.125 2.00e-02 2.50e+03 1.31e-01 2.59e+02 pdb=" CD GLN B 317 " -0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN B 317 " -0.114 2.00e-02 2.50e+03 pdb=" NE2 GLN B 317 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN B 317 " 0.197 2.00e-02 2.50e+03 pdb="HE22 GLN B 317 " -0.190 2.00e-02 2.50e+03 ... (remaining 1268 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 727 2.22 - 2.82: 18833 2.82 - 3.41: 25416 3.41 - 4.01: 34022 4.01 - 4.60: 52869 Nonbonded interactions: 131867 Sorted by model distance: nonbonded pdb=" HH TYR B 499 " pdb=" OD2 ASP B 507 " model vdw 1.628 2.450 nonbonded pdb="HH22 ARG B 125 " pdb=" O ASN B 336 " model vdw 1.642 2.450 nonbonded pdb=" O GLN B 611 " pdb=" HE1 TRP B 617 " model vdw 1.647 2.450 nonbonded pdb=" OE2 GLU B 428 " pdb="HH22 ARG B 445 " model vdw 1.667 2.450 nonbonded pdb=" O VAL B 107 " pdb=" HH TYR B 519 " model vdw 1.695 2.450 ... (remaining 131862 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: 2.350 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: 0.170 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.280 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.006 0.087 4600 Z= 0.347 Angle : 0.719 12.345 6300 Z= 0.419 Chirality : 0.041 0.283 722 Planarity : 0.022 0.488 750 Dihedral : 15.975 123.651 1808 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.87 % Allowed : 14.63 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.38), residues: 542 helix: 1.09 (0.27), residues: 377 sheet: None (None), residues: 0 loop : 0.99 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 238 HIS 0.002 0.000 HIS B 616 PHE 0.013 0.001 PHE B 365 TYR 0.007 0.001 TYR B 575 ARG 0.012 0.001 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7159 (tt0) cc_final: 0.6793 (pt0) REVERT: B 239 GLN cc_start: 0.7865 (mp10) cc_final: 0.7628 (mt0) REVERT: B 295 ARG cc_start: 0.7225 (ttm-80) cc_final: 0.6746 (mtm-85) REVERT: B 360 SER cc_start: 0.8702 (m) cc_final: 0.8474 (p) REVERT: B 483 SER cc_start: 0.8544 (OUTLIER) cc_final: 0.8292 (p) REVERT: B 544 ARG cc_start: 0.6954 (mtm-85) cc_final: 0.6689 (mtm-85) outliers start: 4 outliers final: 3 residues processed: 76 average time/residue: 2.1307 time to fit residues: 169.3263 Evaluate side-chains 67 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 568 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN B 444 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.093838 restraints weight = 14949.996| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.61 r_work: 0.2930 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4600 Z= 0.209 Angle : 0.511 4.502 6300 Z= 0.264 Chirality : 0.036 0.127 722 Planarity : 0.008 0.185 750 Dihedral : 7.840 59.496 891 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.09 % Allowed : 13.97 % Favored : 84.93 % 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: 1.43 (0.37), residues: 542 helix: 1.12 (0.26), residues: 395 sheet: None (None), residues: 0 loop : 0.79 (0.59), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 238 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.001 PHE B 365 TYR 0.010 0.001 TYR B 252 ARG 0.007 0.001 ARG B 443 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7665 (tt0) cc_final: 0.7430 (pt0) REVERT: B 295 ARG cc_start: 0.7616 (ttm-80) cc_final: 0.7125 (mtp180) REVERT: B 483 SER cc_start: 0.8563 (OUTLIER) cc_final: 0.8354 (p) REVERT: B 544 ARG cc_start: 0.7154 (mtm-85) cc_final: 0.6890 (mtm-85) outliers start: 5 outliers final: 2 residues processed: 66 average time/residue: 2.2836 time to fit residues: 158.7846 Evaluate side-chains 62 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 568 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.113287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.093030 restraints weight = 15144.800| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.61 r_work: 0.2892 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4600 Z= 0.226 Angle : 0.490 4.478 6300 Z= 0.256 Chirality : 0.036 0.131 722 Planarity : 0.005 0.060 750 Dihedral : 7.440 59.402 890 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.09 % Allowed : 14.85 % Favored : 84.06 % 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: 1.43 (0.37), residues: 542 helix: 1.18 (0.26), residues: 394 sheet: None (None), residues: 0 loop : 0.60 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 132 HIS 0.006 0.001 HIS B 225 PHE 0.014 0.001 PHE B 365 TYR 0.010 0.001 TYR B 252 ARG 0.008 0.001 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7769 (tt0) cc_final: 0.7503 (pt0) REVERT: B 295 ARG cc_start: 0.7655 (ttm-80) cc_final: 0.7138 (mtp180) REVERT: B 483 SER cc_start: 0.8565 (OUTLIER) cc_final: 0.8354 (p) REVERT: B 544 ARG cc_start: 0.7225 (mtm-85) cc_final: 0.6950 (mtm-85) outliers start: 5 outliers final: 2 residues processed: 59 average time/residue: 2.1550 time to fit residues: 133.2752 Evaluate side-chains 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 568 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.115962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.095964 restraints weight = 14941.378| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.58 r_work: 0.2919 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4600 Z= 0.241 Angle : 0.489 4.485 6300 Z= 0.256 Chirality : 0.037 0.133 722 Planarity : 0.005 0.058 750 Dihedral : 7.315 59.895 890 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.87 % Allowed : 14.85 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.37), residues: 542 helix: 1.17 (0.26), residues: 394 sheet: None (None), residues: 0 loop : 0.54 (0.57), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.002 0.001 HIS B 225 PHE 0.015 0.001 PHE B 365 TYR 0.010 0.001 TYR B 252 ARG 0.009 0.001 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7768 (tt0) cc_final: 0.7546 (pt0) REVERT: B 295 ARG cc_start: 0.7667 (ttm-80) cc_final: 0.7402 (mtm-85) REVERT: B 544 ARG cc_start: 0.7223 (mtm-85) cc_final: 0.6951 (mtm-85) outliers start: 4 outliers final: 2 residues processed: 61 average time/residue: 2.3142 time to fit residues: 147.6131 Evaluate side-chains 58 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 568 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.116512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.096621 restraints weight = 14894.239| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.58 r_work: 0.2897 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4600 Z= 0.192 Angle : 0.468 4.448 6300 Z= 0.246 Chirality : 0.036 0.128 722 Planarity : 0.005 0.062 750 Dihedral : 7.024 58.603 889 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.66 % Allowed : 15.50 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.37), residues: 542 helix: 1.26 (0.26), residues: 394 sheet: None (None), residues: 0 loop : 0.55 (0.56), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 238 HIS 0.002 0.001 HIS B 223 PHE 0.014 0.001 PHE B 365 TYR 0.009 0.001 TYR B 252 ARG 0.007 0.000 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7736 (tt0) cc_final: 0.7412 (pt0) REVERT: B 226 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8104 (mt0) REVERT: B 295 ARG cc_start: 0.7579 (ttm-80) cc_final: 0.7020 (mtp180) REVERT: B 544 ARG cc_start: 0.7141 (mtm-85) cc_final: 0.6846 (mtm-85) outliers start: 3 outliers final: 2 residues processed: 58 average time/residue: 2.4707 time to fit residues: 150.1226 Evaluate side-chains 58 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 429 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.096674 restraints weight = 14875.820| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.58 r_work: 0.2877 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4600 Z= 0.202 Angle : 0.468 4.466 6300 Z= 0.245 Chirality : 0.036 0.128 722 Planarity : 0.005 0.069 750 Dihedral : 6.915 59.568 888 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.66 % Allowed : 15.28 % Favored : 84.06 % 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: 1.52 (0.37), residues: 542 helix: 1.28 (0.26), residues: 394 sheet: None (None), residues: 0 loop : 0.52 (0.56), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 132 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.001 PHE B 365 TYR 0.009 0.001 TYR B 252 ARG 0.011 0.001 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7661 (tt0) cc_final: 0.7203 (pt0) REVERT: B 295 ARG cc_start: 0.7408 (ttm-80) cc_final: 0.7091 (mtm-85) REVERT: B 544 ARG cc_start: 0.7014 (mtm-85) cc_final: 0.6680 (mtm-85) outliers start: 3 outliers final: 1 residues processed: 59 average time/residue: 2.4445 time to fit residues: 150.3491 Evaluate side-chains 59 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.096477 restraints weight = 15079.182| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.59 r_work: 0.2873 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4600 Z= 0.215 Angle : 0.472 4.482 6300 Z= 0.247 Chirality : 0.036 0.129 722 Planarity : 0.005 0.070 750 Dihedral : 6.937 59.519 888 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.44 % Allowed : 15.28 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.37), residues: 542 helix: 1.25 (0.26), residues: 396 sheet: None (None), residues: 0 loop : 0.32 (0.55), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 132 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.001 PHE B 365 TYR 0.009 0.001 TYR B 252 ARG 0.010 0.001 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7693 (tt0) cc_final: 0.7214 (pt0) REVERT: B 295 ARG cc_start: 0.7401 (ttm-80) cc_final: 0.7083 (mtm-85) REVERT: B 443 ARG cc_start: 0.7374 (mtm-85) cc_final: 0.7158 (mtp180) REVERT: B 544 ARG cc_start: 0.7000 (mtm-85) cc_final: 0.6661 (mtm-85) outliers start: 2 outliers final: 2 residues processed: 58 average time/residue: 2.3581 time to fit residues: 142.9191 Evaluate side-chains 58 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 429 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.116526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.096573 restraints weight = 15197.807| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.59 r_work: 0.2901 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4600 Z= 0.206 Angle : 0.469 4.473 6300 Z= 0.246 Chirality : 0.036 0.128 722 Planarity : 0.005 0.076 750 Dihedral : 6.892 58.610 888 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.87 % Allowed : 15.28 % Favored : 83.84 % 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: 1.45 (0.37), residues: 542 helix: 1.27 (0.26), residues: 396 sheet: None (None), residues: 0 loop : 0.35 (0.55), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 132 HIS 0.002 0.001 HIS B 225 PHE 0.014 0.001 PHE B 365 TYR 0.009 0.001 TYR B 252 ARG 0.011 0.001 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7779 (tt0) cc_final: 0.7393 (pt0) REVERT: B 295 ARG cc_start: 0.7580 (ttm-80) cc_final: 0.7286 (mtm-85) REVERT: B 443 ARG cc_start: 0.7447 (mtm-85) cc_final: 0.7240 (mtp180) REVERT: B 544 ARG cc_start: 0.7133 (mtm-85) cc_final: 0.6831 (mtm-85) outliers start: 4 outliers final: 2 residues processed: 60 average time/residue: 2.3865 time to fit residues: 149.3548 Evaluate side-chains 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 453 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.116945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.097095 restraints weight = 15026.369| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.59 r_work: 0.2967 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4600 Z= 0.185 Angle : 0.462 4.450 6300 Z= 0.242 Chirality : 0.035 0.127 722 Planarity : 0.005 0.079 750 Dihedral : 6.787 57.913 888 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.44 % Allowed : 15.72 % Favored : 83.84 % 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: 1.47 (0.37), residues: 542 helix: 1.29 (0.26), residues: 397 sheet: None (None), residues: 0 loop : 0.33 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 238 HIS 0.002 0.001 HIS B 225 PHE 0.013 0.001 PHE B 365 TYR 0.009 0.001 TYR B 252 ARG 0.013 0.001 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7824 (tt0) cc_final: 0.7542 (pt0) REVERT: B 295 ARG cc_start: 0.7674 (ttm-80) cc_final: 0.7399 (mtm-85) REVERT: B 443 ARG cc_start: 0.7473 (mtm-85) cc_final: 0.7272 (mtp180) REVERT: B 544 ARG cc_start: 0.7199 (mtm-85) cc_final: 0.6929 (mtm-85) outliers start: 2 outliers final: 2 residues processed: 57 average time/residue: 2.2531 time to fit residues: 135.0191 Evaluate side-chains 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 453 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.097030 restraints weight = 15052.557| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.59 r_work: 0.2964 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4600 Z= 0.190 Angle : 0.465 4.452 6300 Z= 0.243 Chirality : 0.036 0.160 722 Planarity : 0.005 0.080 750 Dihedral : 6.765 57.380 888 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.44 % Allowed : 15.94 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.37), residues: 542 helix: 1.31 (0.26), residues: 397 sheet: None (None), residues: 0 loop : 0.32 (0.55), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 132 HIS 0.002 0.001 HIS B 225 PHE 0.013 0.001 PHE B 365 TYR 0.009 0.001 TYR B 252 ARG 0.013 0.001 ARG B 615 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 GLU cc_start: 0.7837 (tt0) cc_final: 0.7553 (pt0) REVERT: B 295 ARG cc_start: 0.7685 (ttm-80) cc_final: 0.7253 (mtp180) REVERT: B 544 ARG cc_start: 0.7210 (mtm-85) cc_final: 0.6886 (mtm-85) outliers start: 2 outliers final: 2 residues processed: 57 average time/residue: 2.2802 time to fit residues: 136.2432 Evaluate side-chains 57 residues out of total 458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 453 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 16 optimal weight: 0.1980 chunk 22 optimal weight: 0.0970 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.118613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.098895 restraints weight = 15024.366| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.59 r_work: 0.2994 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4600 Z= 0.140 Angle : 0.441 4.394 6300 Z= 0.230 Chirality : 0.035 0.126 722 Planarity : 0.005 0.076 750 Dihedral : 6.414 56.338 888 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.44 % Allowed : 15.72 % Favored : 83.84 % 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: 1.67 (0.37), residues: 542 helix: 1.43 (0.27), residues: 397 sheet: None (None), residues: 0 loop : 0.41 (0.56), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 238 HIS 0.002 0.001 HIS B 225 PHE 0.011 0.001 PHE B 365 TYR 0.007 0.001 TYR B 252 ARG 0.015 0.001 ARG B 615 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6599.31 seconds wall clock time: 114 minutes 30.60 seconds (6870.60 seconds total)