Starting phenix.real_space_refine on Mon May 6 17:11:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsn_18637/05_2024/8qsn_18637.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsn_18637/05_2024/8qsn_18637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsn_18637/05_2024/8qsn_18637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsn_18637/05_2024/8qsn_18637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsn_18637/05_2024/8qsn_18637.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsn_18637/05_2024/8qsn_18637.pdb" } resolution = 3.54 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= 0.013 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 20 5.16 5 C 2377 2.51 5 N 573 2.21 5 O 609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 3579 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3579 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 18, 'TRANS': 445} Chain breaks: 3 Time building chain proxies: 2.48, per 1000 atoms: 0.69 Number of scatterers: 3579 At special positions: 0 Unit cell: (80.465, 70.015, 65.835, 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 20 16.00 O 609 8.00 N 573 7.00 C 2377 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: 1.56 Conformation dependent library (CDL) restraints added in 821.9 milliseconds 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 846 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 83.4% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 33 through 57 removed outlier: 4.287A pdb=" N ASN A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 70 through 98 removed outlier: 3.899A pdb=" N SER A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 102 through 118 Processing helix chain 'A' and resid 156 through 183 removed outlier: 4.226A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.629A pdb=" N VAL A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.818A pdb=" N THR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 246 removed outlier: 3.931A pdb=" N GLY A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Proline residue: A 229 - end of helix removed outlier: 3.638A pdb=" N VAL A 246 " --> pdb=" O CYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 273 Processing helix chain 'A' and resid 297 through 305 removed outlier: 3.954A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY A 305 " --> pdb=" O MET A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 347 removed outlier: 3.942A pdb=" N VAL A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Proline residue: A 323 - end of helix Proline residue: A 330 - end of helix removed outlier: 3.691A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 349 No H-bonds generated for 'chain 'A' and resid 348 through 349' Processing helix chain 'A' and resid 365 through 366 No H-bonds generated for 'chain 'A' and resid 365 through 366' Processing helix chain 'A' and resid 367 through 396 removed outlier: 3.958A pdb=" N ASP A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) Proline residue: A 382 - end of helix removed outlier: 5.109A pdb=" N ASP A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Proline residue: A 390 - end of helix Processing helix chain 'A' and resid 400 through 431 removed outlier: 3.528A pdb=" N LYS A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 removed outlier: 4.034A pdb=" N TRP A 453 " --> pdb=" O SER A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 454 through 468 Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 484 through 510 Processing helix chain 'A' and resid 531 through 560 removed outlier: 3.573A pdb=" N HIS A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 439 281 hydrogen bonds defined for protein. 837 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: 1.08 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1081 1.34 - 1.46: 817 1.46 - 1.58: 1743 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 3672 Sorted by residual: bond pdb=" CB PRO A 399 " pdb=" CG PRO A 399 " ideal model delta sigma weight residual 1.492 1.537 -0.045 5.00e-02 4.00e+02 8.11e-01 bond pdb=" CA ILE A 329 " pdb=" C ILE A 329 " ideal model delta sigma weight residual 1.523 1.531 -0.008 9.20e-03 1.18e+04 7.12e-01 bond pdb=" C VAL A 246 " pdb=" O VAL A 246 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 6.67e-01 bond pdb=" CB PRO A 306 " pdb=" CG PRO A 306 " ideal model delta sigma weight residual 1.492 1.524 -0.032 5.00e-02 4.00e+02 4.05e-01 bond pdb=" N VAL A 322 " pdb=" CA VAL A 322 " ideal model delta sigma weight residual 1.463 1.470 -0.007 1.18e-02 7.18e+03 4.00e-01 ... (remaining 3667 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.07: 97 107.07 - 113.80: 2051 113.80 - 120.53: 1489 120.53 - 127.26: 1307 127.26 - 133.99: 41 Bond angle restraints: 4985 Sorted by residual: angle pdb=" C PHE A 247 " pdb=" N ILE A 248 " pdb=" CA ILE A 248 " ideal model delta sigma weight residual 121.97 125.78 -3.81 1.80e+00 3.09e-01 4.48e+00 angle pdb=" N ILE A 466 " pdb=" CA ILE A 466 " pdb=" C ILE A 466 " ideal model delta sigma weight residual 113.00 110.27 2.73 1.30e+00 5.92e-01 4.42e+00 angle pdb=" N GLU A 309 " pdb=" CA GLU A 309 " pdb=" C GLU A 309 " ideal model delta sigma weight residual 110.80 115.23 -4.43 2.13e+00 2.20e-01 4.32e+00 angle pdb=" C THR A 308 " pdb=" N GLU A 309 " pdb=" CA GLU A 309 " ideal model delta sigma weight residual 121.54 125.26 -3.72 1.91e+00 2.74e-01 3.79e+00 angle pdb=" N ALA A 468 " pdb=" CA ALA A 468 " pdb=" C ALA A 468 " ideal model delta sigma weight residual 111.02 113.92 -2.90 1.52e+00 4.33e-01 3.64e+00 ... (remaining 4980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.62: 1970 14.62 - 29.24: 99 29.24 - 43.87: 29 43.87 - 58.49: 8 58.49 - 73.11: 2 Dihedral angle restraints: 2108 sinusoidal: 785 harmonic: 1323 Sorted by residual: dihedral pdb=" CA THR A 308 " pdb=" C THR A 308 " pdb=" N GLU A 309 " pdb=" CA GLU A 309 " ideal model delta harmonic sigma weight residual -180.00 -163.82 -16.18 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ARG A 33 " pdb=" CB ARG A 33 " pdb=" CG ARG A 33 " pdb=" CD ARG A 33 " ideal model delta sinusoidal sigma weight residual -60.00 -115.47 55.47 3 1.50e+01 4.44e-03 9.35e+00 dihedral pdb=" CA ARG A 104 " pdb=" CB ARG A 104 " pdb=" CG ARG A 104 " pdb=" CD ARG A 104 " ideal model delta sinusoidal sigma weight residual 180.00 127.75 52.25 3 1.50e+01 4.44e-03 9.10e+00 ... (remaining 2105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 389 0.025 - 0.050: 100 0.050 - 0.075: 55 0.075 - 0.101: 24 0.101 - 0.126: 6 Chirality restraints: 574 Sorted by residual: chirality pdb=" CA THR A 176 " pdb=" N THR A 176 " pdb=" C THR A 176 " pdb=" CB THR A 176 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA ILE A 439 " pdb=" N ILE A 439 " pdb=" C ILE A 439 " pdb=" CB ILE A 439 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ILE A 435 " pdb=" N ILE A 435 " pdb=" C ILE A 435 " pdb=" CB ILE A 435 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.12e-01 ... (remaining 571 not shown) Planarity restraints: 611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 238 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C VAL A 238 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL A 238 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 239 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 239 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C VAL A 239 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL A 239 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 240 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 237 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C PHE A 237 " 0.026 2.00e-02 2.50e+03 pdb=" O PHE A 237 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 238 " -0.009 2.00e-02 2.50e+03 ... (remaining 608 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 887 2.80 - 3.32: 3828 3.32 - 3.85: 5935 3.85 - 4.37: 6627 4.37 - 4.90: 11289 Nonbonded interactions: 28566 Sorted by model distance: nonbonded pdb=" O LEU A 264 " pdb=" OG SER A 267 " model vdw 2.269 2.440 nonbonded pdb=" O ILE A 461 " pdb=" OG SER A 464 " model vdw 2.272 2.440 nonbonded pdb=" OG1 THR A 333 " pdb=" O GLY A 499 " model vdw 2.305 2.440 nonbonded pdb=" O LYS A 262 " pdb=" OG1 THR A 265 " model vdw 2.316 2.440 nonbonded pdb=" O CYS A 242 " pdb=" OG SER A 245 " model vdw 2.326 2.440 ... (remaining 28561 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: 0.790 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: 2.840 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.160 Find NCS groups from input model: 0.100 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.002 0.045 3672 Z= 0.125 Angle : 0.482 5.910 4985 Z= 0.259 Chirality : 0.034 0.126 574 Planarity : 0.004 0.029 611 Dihedral : 10.371 73.110 1262 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.75 % Allowed : 6.17 % Favored : 90.08 % 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: 2.22 (0.41), residues: 456 helix: 2.29 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -1.69 (0.60), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 332 HIS 0.001 0.000 HIS A 348 PHE 0.009 0.001 PHE A 198 TYR 0.006 0.001 TYR A 52 ARG 0.001 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6367 (mtm-85) REVERT: A 44 GLU cc_start: 0.9074 (tp30) cc_final: 0.8872 (tp30) REVERT: A 47 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8533 (tm-30) REVERT: A 91 PHE cc_start: 0.8834 (m-80) cc_final: 0.8615 (m-10) REVERT: A 198 PHE cc_start: 0.9062 (t80) cc_final: 0.8784 (t80) REVERT: A 200 TRP cc_start: 0.9108 (t60) cc_final: 0.8457 (t60) REVERT: A 313 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8758 (mm-30) REVERT: A 342 TYR cc_start: 0.8828 (m-10) cc_final: 0.8493 (m-80) REVERT: A 369 LEU cc_start: 0.8668 (mt) cc_final: 0.8262 (mt) REVERT: A 427 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8093 (mt) REVERT: A 451 LEU cc_start: 0.9283 (tp) cc_final: 0.9027 (mp) REVERT: A 454 GLN cc_start: 0.8598 (tp40) cc_final: 0.8199 (tp40) REVERT: A 457 GLN cc_start: 0.7851 (pt0) cc_final: 0.6235 (pt0) REVERT: A 474 GLU cc_start: 0.8866 (mt-10) cc_final: 0.7919 (mt-10) REVERT: A 535 TYR cc_start: 0.8685 (t80) cc_final: 0.8193 (t80) outliers start: 14 outliers final: 3 residues processed: 181 average time/residue: 0.1726 time to fit residues: 37.1114 Evaluate side-chains 105 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 427 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A 345 GLN ** A 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3672 Z= 0.225 Angle : 0.706 9.786 4985 Z= 0.333 Chirality : 0.041 0.167 574 Planarity : 0.005 0.050 611 Dihedral : 5.662 54.570 502 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.83 % Allowed : 17.69 % Favored : 77.48 % 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: 2.48 (0.40), residues: 456 helix: 2.39 (0.27), residues: 364 sheet: None (None), residues: 0 loop : -1.59 (0.59), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 69 HIS 0.003 0.001 HIS A 521 PHE 0.033 0.002 PHE A 417 TYR 0.013 0.002 TYR A 477 ARG 0.010 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 0.366 Fit side-chains REVERT: A 33 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6527 (ptp-170) REVERT: A 91 PHE cc_start: 0.8871 (m-80) cc_final: 0.8666 (m-10) REVERT: A 200 TRP cc_start: 0.9086 (t60) cc_final: 0.8423 (t60) REVERT: A 235 LEU cc_start: 0.9545 (mt) cc_final: 0.8964 (tp) REVERT: A 301 MET cc_start: 0.5867 (tpt) cc_final: 0.5563 (tmm) REVERT: A 331 TYR cc_start: 0.8977 (t80) cc_final: 0.8503 (t80) REVERT: A 427 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8490 (mt) REVERT: A 535 TYR cc_start: 0.8920 (t80) cc_final: 0.8523 (t80) outliers start: 18 outliers final: 11 residues processed: 115 average time/residue: 0.1154 time to fit residues: 17.3542 Evaluate side-chains 100 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 532 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 0.0270 chunk 41 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 0.0040 chunk 31 optimal weight: 0.9990 overall best weight: 0.5852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3672 Z= 0.177 Angle : 0.694 11.785 4985 Z= 0.328 Chirality : 0.039 0.159 574 Planarity : 0.005 0.048 611 Dihedral : 5.834 54.941 500 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.02 % Allowed : 22.25 % Favored : 73.73 % 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: 2.26 (0.40), residues: 456 helix: 2.17 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -1.81 (0.64), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 69 HIS 0.001 0.000 HIS A 521 PHE 0.050 0.002 PHE A 372 TYR 0.018 0.002 TYR A 335 ARG 0.004 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.411 Fit side-chains REVERT: A 33 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6543 (ptp-170) REVERT: A 200 TRP cc_start: 0.9092 (t60) cc_final: 0.8434 (t60) REVERT: A 301 MET cc_start: 0.6250 (tpt) cc_final: 0.6003 (tmm) REVERT: A 307 PHE cc_start: 0.3775 (OUTLIER) cc_final: 0.3504 (m-80) REVERT: A 331 TYR cc_start: 0.9038 (t80) cc_final: 0.8603 (t80) REVERT: A 427 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8558 (mt) REVERT: A 454 GLN cc_start: 0.8681 (tp40) cc_final: 0.8445 (mm-40) REVERT: A 535 TYR cc_start: 0.8901 (t80) cc_final: 0.8479 (t80) outliers start: 15 outliers final: 8 residues processed: 106 average time/residue: 0.1121 time to fit residues: 15.5700 Evaluate side-chains 102 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 532 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.4980 chunk 4 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3672 Z= 0.223 Angle : 0.710 12.352 4985 Z= 0.343 Chirality : 0.041 0.156 574 Planarity : 0.004 0.036 611 Dihedral : 5.400 54.124 499 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.09 % Allowed : 23.32 % Favored : 71.58 % 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: 2.10 (0.41), residues: 456 helix: 2.09 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.89 (0.67), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 368 HIS 0.001 0.000 HIS A 445 PHE 0.056 0.002 PHE A 372 TYR 0.015 0.001 TYR A 335 ARG 0.003 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6523 (ptp-170) REVERT: A 200 TRP cc_start: 0.9144 (t60) cc_final: 0.8472 (t60) REVERT: A 301 MET cc_start: 0.6424 (tpt) cc_final: 0.6132 (tmm) REVERT: A 310 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7494 (tm-30) REVERT: A 427 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8665 (mt) REVERT: A 474 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8176 (mt-10) REVERT: A 535 TYR cc_start: 0.8975 (t80) cc_final: 0.8657 (t80) outliers start: 19 outliers final: 11 residues processed: 114 average time/residue: 0.1276 time to fit residues: 18.4943 Evaluate side-chains 104 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 457 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.0570 chunk 18 optimal weight: 0.0020 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.5306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3672 Z= 0.172 Angle : 0.708 11.472 4985 Z= 0.333 Chirality : 0.040 0.160 574 Planarity : 0.004 0.041 611 Dihedral : 5.443 54.397 499 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.56 % Allowed : 25.74 % Favored : 69.71 % 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: 2.06 (0.41), residues: 456 helix: 2.08 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -1.98 (0.67), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 69 HIS 0.001 0.000 HIS A 303 PHE 0.060 0.002 PHE A 372 TYR 0.018 0.001 TYR A 444 ARG 0.003 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.433 Fit side-chains REVERT: A 33 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6511 (ptp-170) REVERT: A 200 TRP cc_start: 0.9124 (t60) cc_final: 0.8422 (t60) REVERT: A 220 VAL cc_start: 0.7489 (OUTLIER) cc_final: 0.7283 (m) REVERT: A 301 MET cc_start: 0.6288 (tpt) cc_final: 0.6040 (tmm) REVERT: A 331 TYR cc_start: 0.9155 (t80) cc_final: 0.8770 (t80) REVERT: A 371 MET cc_start: 0.8823 (mtt) cc_final: 0.8573 (ptp) REVERT: A 427 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8607 (mt) REVERT: A 474 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8115 (mt-10) REVERT: A 535 TYR cc_start: 0.8924 (t80) cc_final: 0.8606 (t80) outliers start: 17 outliers final: 6 residues processed: 116 average time/residue: 0.1251 time to fit residues: 18.6335 Evaluate side-chains 105 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 5 optimal weight: 0.0670 chunk 25 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3672 Z= 0.177 Angle : 0.770 13.590 4985 Z= 0.347 Chirality : 0.041 0.177 574 Planarity : 0.004 0.039 611 Dihedral : 5.471 54.187 499 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.49 % Allowed : 28.95 % Favored : 67.56 % 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: 1.94 (0.41), residues: 456 helix: 2.00 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -2.05 (0.68), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.000 0.000 HIS A 303 PHE 0.051 0.001 PHE A 372 TYR 0.014 0.001 TYR A 477 ARG 0.003 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6504 (ptp-170) REVERT: A 200 TRP cc_start: 0.9157 (t60) cc_final: 0.8449 (t60) REVERT: A 220 VAL cc_start: 0.7554 (OUTLIER) cc_final: 0.7353 (m) REVERT: A 301 MET cc_start: 0.6373 (tpt) cc_final: 0.6171 (tmm) REVERT: A 310 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7153 (tm-30) REVERT: A 371 MET cc_start: 0.8787 (mtt) cc_final: 0.8336 (mmm) REVERT: A 427 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8627 (mt) REVERT: A 474 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8149 (mt-10) REVERT: A 535 TYR cc_start: 0.8944 (t80) cc_final: 0.8608 (t80) outliers start: 13 outliers final: 7 residues processed: 110 average time/residue: 0.1135 time to fit residues: 16.5198 Evaluate side-chains 102 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3672 Z= 0.183 Angle : 0.767 12.387 4985 Z= 0.342 Chirality : 0.040 0.150 574 Planarity : 0.004 0.042 611 Dihedral : 5.509 54.288 499 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.75 % Allowed : 28.69 % Favored : 67.56 % 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: 1.96 (0.41), residues: 456 helix: 2.02 (0.27), residues: 371 sheet: None (None), residues: 0 loop : -2.06 (0.68), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 332 HIS 0.001 0.000 HIS A 521 PHE 0.042 0.002 PHE A 372 TYR 0.017 0.001 TYR A 477 ARG 0.004 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.445 Fit side-chains REVERT: A 33 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6504 (ptp-170) REVERT: A 110 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9384 (tt) REVERT: A 200 TRP cc_start: 0.9158 (t60) cc_final: 0.8433 (t60) REVERT: A 331 TYR cc_start: 0.9164 (t80) cc_final: 0.8905 (t80) REVERT: A 371 MET cc_start: 0.8797 (mtt) cc_final: 0.8394 (mmm) REVERT: A 427 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8420 (mt) REVERT: A 474 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8155 (mt-10) REVERT: A 535 TYR cc_start: 0.8942 (t80) cc_final: 0.8674 (t80) outliers start: 14 outliers final: 7 residues processed: 103 average time/residue: 0.1118 time to fit residues: 15.2258 Evaluate side-chains 101 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 0.0470 chunk 40 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 41 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3672 Z= 0.196 Angle : 0.823 15.074 4985 Z= 0.367 Chirality : 0.041 0.158 574 Planarity : 0.004 0.038 611 Dihedral : 5.563 54.262 499 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.75 % Allowed : 29.49 % Favored : 66.76 % 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: 1.95 (0.41), residues: 456 helix: 2.01 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -2.02 (0.67), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 332 HIS 0.001 0.000 HIS A 303 PHE 0.036 0.001 PHE A 372 TYR 0.015 0.001 TYR A 477 ARG 0.004 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.432 Fit side-chains REVERT: A 33 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6504 (ptp-170) REVERT: A 110 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9411 (tt) REVERT: A 200 TRP cc_start: 0.9129 (t60) cc_final: 0.8391 (t60) REVERT: A 331 TYR cc_start: 0.9162 (t80) cc_final: 0.8889 (t80) REVERT: A 427 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8371 (mt) REVERT: A 474 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8143 (mt-10) REVERT: A 535 TYR cc_start: 0.8943 (t80) cc_final: 0.8678 (t80) outliers start: 14 outliers final: 10 residues processed: 105 average time/residue: 0.1086 time to fit residues: 15.1187 Evaluate side-chains 105 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 0.0670 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3672 Z= 0.191 Angle : 0.830 13.531 4985 Z= 0.373 Chirality : 0.042 0.205 574 Planarity : 0.004 0.038 611 Dihedral : 5.600 54.255 499 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.49 % Allowed : 29.22 % Favored : 67.29 % 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: 1.97 (0.40), residues: 456 helix: 2.04 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -1.88 (0.65), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 332 HIS 0.001 0.000 HIS A 521 PHE 0.042 0.002 PHE A 372 TYR 0.025 0.001 TYR A 477 ARG 0.004 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.388 Fit side-chains REVERT: A 33 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6508 (ptp-170) REVERT: A 200 TRP cc_start: 0.9117 (t60) cc_final: 0.8427 (t60) REVERT: A 331 TYR cc_start: 0.9149 (t80) cc_final: 0.8885 (t80) REVERT: A 371 MET cc_start: 0.8688 (mtt) cc_final: 0.8072 (mmm) REVERT: A 427 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8383 (mt) REVERT: A 474 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8305 (mt-10) REVERT: A 535 TYR cc_start: 0.8924 (t80) cc_final: 0.8680 (t80) outliers start: 13 outliers final: 10 residues processed: 104 average time/residue: 0.1167 time to fit residues: 16.1667 Evaluate side-chains 106 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.0060 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 33 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3672 Z= 0.191 Angle : 0.862 13.058 4985 Z= 0.389 Chirality : 0.042 0.200 574 Planarity : 0.004 0.037 611 Dihedral : 5.611 54.212 499 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.95 % Allowed : 30.03 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.40), residues: 456 helix: 1.93 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -2.08 (0.67), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 368 HIS 0.001 0.000 HIS A 521 PHE 0.052 0.002 PHE A 372 TYR 0.016 0.001 TYR A 477 ARG 0.003 0.000 ARG A 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.438 Fit side-chains REVERT: A 33 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6807 (mtt180) REVERT: A 200 TRP cc_start: 0.9108 (t60) cc_final: 0.8438 (t60) REVERT: A 237 PHE cc_start: 0.9507 (t80) cc_final: 0.9256 (m-80) REVERT: A 331 TYR cc_start: 0.9138 (t80) cc_final: 0.8890 (t80) REVERT: A 427 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8337 (mt) REVERT: A 474 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8280 (mt-10) REVERT: A 535 TYR cc_start: 0.8881 (t80) cc_final: 0.8651 (t80) outliers start: 11 outliers final: 9 residues processed: 102 average time/residue: 0.1115 time to fit residues: 14.9268 Evaluate side-chains 104 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 24 optimal weight: 0.0270 chunk 31 optimal weight: 0.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 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 = 0.3915 r_free = 0.3915 target = 0.096792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.082951 restraints weight = 13652.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.085101 restraints weight = 8092.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.086590 restraints weight = 5492.120| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3672 Z= 0.197 Angle : 0.849 12.715 4985 Z= 0.387 Chirality : 0.043 0.251 574 Planarity : 0.004 0.037 611 Dihedral : 5.668 54.240 499 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.68 % Allowed : 31.10 % Favored : 66.22 % 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: 1.78 (0.41), residues: 456 helix: 1.90 (0.27), residues: 370 sheet: None (None), residues: 0 loop : -2.14 (0.67), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 332 HIS 0.001 0.000 HIS A 395 PHE 0.057 0.002 PHE A 372 TYR 0.015 0.001 TYR A 477 ARG 0.005 0.000 ARG A 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1189.15 seconds wall clock time: 22 minutes 11.74 seconds (1331.74 seconds total)